Package: 2b-rad Version: 2.0-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: bbtools, bioperl, cd-hit, raxml, shrimp Filename: ./2b-rad_2.0-2lbi_all.deb Size: 28084 MD5sum: 557f6968262cf1189d029ac4b3b06552 SHA1: 7c5b0d538a87bc910f65e8558c126633dc4c10ef SHA256: 6cc54db448ca4ba8b7884cabc542abcf7aa2d11a7a5623c56d3e89e8fcfa93cd Section: science Priority: optional Homepage: http://people.oregonstate.edu/~meyere/2bRAD_analysis2.1.html Description: A collection of scripts for analyzing 2bRAD genotyping data These tools are intended to be used on a high-performance computing cluster. To analyze large numbers of samples in parallel, the user will probably want to submit each job to a job scheduler such as SGE. Original-Maintainer: Eli Meyer Package: abyss Version: 2.1.5-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: make, libc6 (>= 2.14), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 5.2), perl:any, bsdmainutils, libsparsehash-dev Suggests: openmpi-bin Filename: ./abyss_2.1.5-1lbi_amd64.deb Size: 16878028 MD5sum: ca0d626594854d83e25a48f1e033059d SHA1: 05a53f3a5508d419df43288e18d6aa200e5be2d1 SHA256: dc8dc068ccb24e6c994f0e27a3db9bafa3428eeda3cbc10ca63870235c1ce356 Section: science Priority: optional Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Description: de novo, parallel, sequence assembler for short reads ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. Original-Maintainer: Abyss list Package: amos Version: 3.1.0-9lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: perl (>= 5.6.0), python2, libdbi-perl, libstatistics-descriptive-perl, libxml-parser-perl, mummer, expat Filename: ./amos_3.1.0-9lbi_amd64.deb Size: 73628548 MD5sum: ca3e0c49ad396c3fc1c5769fe61b2797 SHA1: 19e4135eac51324ab812b00687b28beff13bf33e SHA256: 713754062f1a4e4fa1e158515f70e7fe9aeb5c747e3937072d140dbce58ff6f7 Section: science Priority: optional Homepage: http://sourceforge.net/apps/mediawiki/amos/ Description: A Modular Open Source Assembler AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. Original-Maintainer: AMOS Package: amphora Version: 2.0-3lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: bioperl (>= 1.6.924), emboss, hmmer (>= 3.0), raxml (>= 7.3.0) Filename: ./amphora_2.0-3lbi_all.deb Size: 8290 MD5sum: 2062711fdedc841db5b1d2416cb42c31 SHA1: bb95b0b7735c7aaaee7b47929ba60efa7f81a349 SHA256: b48befa559447a0efb4832756494b03c4fcff66bfb33b80ba0904adfe666ef6f Section: science Priority: optional Homepage: http://wolbachia.biology.virginia.edu/WuLab/Software.html Description: AutoMated PHylogenOmic infeRence Application AMPHORA is an automated phylogenomic inference application for large-scale protein phylogenetic analysis. It has been applied to automated genome tree construction and metagenomic sequence phylotyping. Original-Maintainer: Martin Wu Package: augustus Version: 3.3.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bcftools, libbamtools-dev, libboost-all-dev, libbz2-dev, libcurl3-dev, libgsl-dev, libhts-dev, liblpsolve55-dev, liblzma-dev, libmysql++-dev, libncurses5-dev, libsqlite3-dev, libssl-dev, libsuitesparse-dev, samtools, tabix, zlib1g-dev Filename: ./augustus_3.3.2-0lbi_amd64.deb Size: 27636484 MD5sum: 251e1f161ad2f8687063ea305cba4fbb SHA1: 9b8d53b095a6d4f254d16a40e5490e208e29203c SHA256: 4b71da18ad3f6721b76921c450081750f5119c508da675a442bb8b9de81261a5 Section: science Priority: optional Homepage: http://bioinf.uni-greifswald.de/augustus/ Description: AUGUSTUS predicts genes in eukaryotic genomic sequences AUGUSTUS is a gene prediction program written by Mario Stanke, Oliver Keller, Stefanie König, Lizzy Gerischer and Katharina Hoff. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and syntenic genomic alignments. Since version 3.0 AUGUSTUS can also predict the genes simultaneously in several aligned genomes. Original-Maintainer: Mario Stanke Package: autofact Version: 3.4-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: bioperl (>= 1.4), libio-string-perl, ncbi-blast+, perl (>= 5.8.1) Filename: ./autofact_3.4-1lbi_all.deb Size: 381370 MD5sum: 2235b7755585bb27b4592f7f05c58dc2 SHA1: 7d042f2dafd23f29dc2b01fef4d61f116c4e5626 SHA256: 0899c66cd2b9adc3a542f0578e55f8447fb84501dffc522d4529a0f1c48ac974 Section: science Priority: optional Homepage: http://megasun.bch.umontreal.ca/Software/AutoFACT.htm Description: Automatic Functional Annotation and Classification Tool AutoFACT can be used to automatically annotate and classify both nucleotide and amino acid sequence data with functional description lines, EC numbers, LOCUS names, GeneOntology terms, KEGG pathways, and COG functional groups. Original-Maintainer: Liisa B. Koski Package: basemount Version: 0.25.2.3265-20221130-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: fuse, libcurl3-gnutls, openssl, bash-completion, psmisc Filename: ./basemount_0.25.2.3265-20221130-0lbi_amd64.deb Size: 4154940 MD5sum: 53f406d407a04f693f346bbcb2961873 SHA1: 311e73bff7c276fde9680c9577873e5010c9c4ec SHA256: f3a1882eea7740063fb8393b8edc4d0e85fdb0833a47fb8b724695ef0b846c24 Section: science Priority: optional Homepage: https://basemount.basespace.illumina.com/ Description: FUSE driver for Illumina BaseSpace accounts BaseMount is a FUSE driver to mount and access Illumina BaseSpace accounts from the command line. Original-Maintainer: Illumina Package: bbtools Version: 37.96-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: default-jre (>= 1.7) Filename: ./bbtools_37.96-2lbi_all.deb Size: 3843284 MD5sum: 2a6decb7b814c6ad1f3b8f2d5a87fa5c SHA1: 16c88d25cad3493b2f9dcaa110d4e08bfcc3a668 SHA256: 44c5e979e9374de54f369cd6c5e265afed0683d8f240220079879b64687d0910 Section: science Priority: optional Homepage: https://jgi.doe.gov/data-and-tools/bbtools/ Description: BBMap short read aligner and other bioinformatic tools BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. Original-Maintainer: BBTools Google Group Package: besst Version: 2.2.4-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-mathstats (>= 0.2.4), python-networkx (>= 1.9), python-pysam (>= 0.7), python-scipy (>= 0.9) Filename: ./besst_2.2.4-1lbi_amd64.deb Size: 127700 MD5sum: b7137faf8ce52def47e6425f74f5ee31 SHA1: bab40ffd9b54dd6d16a19fa9b69053136e95ed1b SHA256: b185870da011c29a94ee776f390b37f5a90f5e8d48b67fea58e3b27e3bfc14df Section: science Priority: optional Homepage: https://github.com/ksahlin/BESST Description: Scaffolder for genomic assemblies BESST can scaffold genomes of all sizes and complexities. BESST fares favorably to the other tested scaffolders on GAGE datasets and outperforms the other methods when library insert size distribution is wide. Original-Maintainer: Kristoffer Sahlin Package: binsanity Version: 0.2.5.10-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: bedtools (>= 2.17), bowtie2, checkm-genome, python-biopython, python-numpy (>= 1.11), python-pandas (>= 0.13.0), python-scikits-learn (>= 0.17), python-scipy (>= 0.13.0), samtools, subread Recommends: hmmer, pplacer Filename: ./binsanity_0.2.5.10-1lbi_all.deb Size: 17004 MD5sum: e643cb18cfa6cc6405460e2445cbd8ad SHA1: 6d83aa0592e9f7a43c7a622393b767e0a3caaa7c SHA256: 59a3258ff98d665f95adc42039548e020750f44a9fb0494a12a4aa39d3fcad83 Section: science Priority: optional Homepage: https://github.com/edgraham/BinSanity Description: Cluster contigs from metagenomic assembly Method to cluster contigs based a biphasic method with coverage and composition. Original-Maintainer: Elaina Graham Package: bio-linux-mview Version: 1.51-3 Architecture: all Maintainer: Tim Booth Installed-Size: 1644 Filename: ./third-party/bio-linux-mview_1.51-3_all.deb Size: 142066 MD5sum: c1ec6d1767d4889ec319064b0c856a15 SHA1: ea17967018aa2895d0181d65819dc99a374da86d SHA256: 6c37b1f2ccd6fcd79f2ba921a7754998101f70c124e019d54b234b5b18c38c53 Section: science Priority: optional Description: Multiple alignment viewer for sequence database search results. MView is a tool for converting the results of a sequence database search (BLAST, FASTA, etc.) into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be processed. . (Repackaged on Mon, 11 Jul 2022 11:23:59 -0300 by dpkg-repack.) Package: bioawk Version: 1.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./bioawk_1.0-0lbi_amd64.deb Size: 125668 MD5sum: cd1e7ee95f9e913188dbbc418cf72ed5 SHA1: 7991731e24a7c5b25579c024a97fd65b7351c0f7 SHA256: 5ccc5db3cbec14d623f28147f37dcbde985e5c0845cf9925c7c375c6d8ea1e95 Section: science Priority: optional Homepage: https://github.com/lh3/bioawk Description: AWK modified for biological data Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk. Original-Maintainer: Heng Li Package: blasr Version: 1.3.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libc6, libgcc1, libhdf5-dev, libstdc++6, zlib1g Filename: ./blasr_1.3.1-0lbi_amd64.deb Size: 1996344 MD5sum: 25afdc2c81297eb73f59dee1180315c8 SHA1: 86f0ba8f55f5ec3260a28bc3728132248b7ac613 SHA256: 624175d002968da07b4094ee3759f19f7cf10549e0a65165a745329ad53aafb4 Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/blasr Description: The PacBio long read aligner blasr is a read mapping program that maps reads to positions in a genome by clustering short exact matches between the read and the genome, and scoring clusters using alignment. The matches are generated by searching all suffixes of a read against the genome using a suffix array. Global chaining methods are used to score clusters of matches. Original-Maintainer: Yuan Li Package: blast2 Source: ncbi-blast+ (2.9.0-2) Version: 1:2.9.0-2 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 22 Depends: ncbi-blast+-legacy Filename: ./third-party/blast2_2.9.0-2_all.deb Size: 4576 MD5sum: bb7c60adb4821c15059e92164e2c87d3 SHA1: a9224966cd358245c98a7c8a9320c5e6137930a3 SHA256: 7d7cd2b846ed87a3310ab2ba9752780c6e6b34a79b97859413d81cdd6ed567b6 Section: oldlibs Priority: optional Multi-Arch: foreign Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ Description: transitional dummy package to ncbi-blast+-legacy This is a transitional dummy package for ncbi-blast+-legacy. It can safely be removed. . (Repackaged on Mon, 02 May 2022 16:16:42 -0300 by dpkg-repack.) Package: busco Version: 5.2.2-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: augustus (>= 3.2), hmmer (>= 3.1), metaeuk, ncbi-blast+ (>= 2.10.1), prodigal, python3 (>= 3.3), python3-biopython, python3-pandas, r-cran-ggplot2, sepp Filename: ./busco_5.2.2-0lbi_all.deb Size: 65002 MD5sum: e5b9e9f4d27eaed81e7326e505fb5465 SHA1: de34d70509576fbd33c1a31c1b6163ca54ee6a6a SHA256: 7df22ec04cfcb569c5d8369702089c5765d0b53bce90087edc4dbf549413c713 Section: science Priority: optional Homepage: http://busco.ezlab.org/ Description: Assessing genome assembly and annotation completeness Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. . Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate dataset for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly-introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets. Original-Maintainer: Evgeny M. Zdobnov Package: cactus Version: 1.0-4lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython, lastz, python-decorator, python-networkx (>= 2), python-networkx (<< 3), python-toil Filename: ./cactus_1.0-4lbi_amd64.deb Size: 84048108 MD5sum: bef47c6faaab897694bb6ab327c0bd85 SHA1: e09d017423b6b61273209f1bb5bb599cfc98d29c SHA256: b6ed9f5311117eefa243809a540bd8f4de075e050b43aa9427e3e7483d2ad0f4 Section: science Priority: optional Homepage: https://github.com/ComparativeGenomicsToolkit/cactus Description: Genome aligner based upon notion of Cactus graphs Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described in https://doi.org/10.1101/gr.123356.111 Original-Maintainer: Joel Armstrong Package: camsa Version: 1.0.0b1-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-biopython, python-blist, python-configargparse, python-enum34, python-jinja2, python-networkx, python-six Filename: ./camsa_1.0.0b1-1lbi_amd64.deb Size: 1845052 MD5sum: 0980d8001ecc892a36537fde4df627e1 SHA1: 9738d30415b39b395a8074873d119def6d4cc6f1 SHA256: ed8d69cb604086f586bcc83c74fd61bc2d6fa46571314b8e169f7965f4adf1a7 Section: science Priority: optional Homepage: https://github.com/compbiol/CAMSA Description: Comparative Analysis and Merging of Scaffold Assemblies CAMSA - is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Original-Maintainer: Sergey Aganezov Package: canu Version: 1.8-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libc6 (>= 2.14), libfilesys-df-perl, libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libstdc++6 (>= 5.2), perl (>= 5.12.0) Recommends: gnuplot Suggests: pbgenomicconsensus, nanopolish Filename: ./canu_1.8-0lbi_amd64.deb Size: 24449892 MD5sum: f7689e90916265225f2005fd0216f593 SHA1: 92c454b7881779c77f99b0cc64a3a4191bdb1ea3 SHA256: a18f841d07d9ef0605c590623833e3b9cc25371c1387c57fae037d60a171b1ae Section: science Priority: optional Homepage: http://canu.readthedocs.org/en/latest/ Description: Single molecule sequence assembler for genomes Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). . Canu is a hierarchical assembly pipeline which runs in four steps: . * Detect overlaps in high-noise sequences using MHAP * Generate corrected sequence consensus * Trim corrected sequences * Assemble trimmed corrected sequences Original-Maintainer: Brian Walenz Package: ccmetagen Version: 1.2.2-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: kma, krona, python3-ete3, python3-pandas Filename: ./ccmetagen_1.2.2-0lbi_all.deb Size: 27780 MD5sum: 69ebcdcc918331f590449a1b152b35fe SHA1: 5dd65d565605bcbb342d6338e871c6dd04c319e4 SHA256: 6cbeb57afde9c654d81efdae3bdfa00e2bc2d17e1616e6d2695d4add35342468 Section: science Priority: optional Homepage: https://github.com/vrmarcelino/CCMetagen Description: Microbiome classification pipeline CCMetagen processes sequence alignments produced with KMA, which implements the ConClave sorting scheme to achieve highly accurate read mappings. The pipeline is fast enough to use the whole NCBI nt collection as reference, facilitating the inclusion of understudied organisms, such as microbial eukaryotes, in metagenome surveys. CCMetagen produces ranked taxonomic results in user-friendly formats that are ready for publication or downstream statistical analyses. Original-Maintainer: Vanessa R. Marcelino Package: cd-hit Version: 4.8.1-4lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: ncbi-blast+, zlib1g-dev Filename: ./cd-hit_4.8.1-4lbi_amd64.deb Size: 975548 MD5sum: e2a9dd101cc5d31b23857219e0066b7d SHA1: a5549b849efff8d9e11b5cb4937455c15e31919f SHA256: 99f481a161ad897c02e1585f6e0f665449ca51257bb697376274aaf5788c6ff6 Section: science Priority: optional Homepage: http://cd-hit.org Description: Clustering and comparing protein or nucleotide sequences CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik's Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute) . CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. Original-Maintainer: Weizhong Li Package: cdbfasta Version: 20100722-2biolinux0.1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 206 Depends: libc6 (>= 2.14), libstdc++6 (>= 4.1.1), zlib1g (>= 1:1.1.4) Filename: ./cdbfasta_20100722-2biolinux0.1_amd64.deb Size: 53948 MD5sum: 11ac1627d9f47accff5855d76a208d50 SHA1: 5c7f4150bd44e7bc1d870e0e96fef537eb9633b2 SHA256: b4c9a0e80f0a53327351c6127dffdfc460d1a5c90b3954a5141e1526008f1645 Section: science Priority: optional Homepage: http://cdbfasta.sourceforge.net/ Description: Constant DataBase indexing and retrieval tools for multi-FASTA files CDB (Constant DataBase) can be used for creating indices for quick retrieval of any particular sequences from large multi-FASTA files. It has the option to compress data records in order to save space. Package: celera Version: 8.3.rc2-5lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: blasr Filename: ./celera_8.3.rc2-5lbi_amd64.deb Size: 14474204 MD5sum: 56068c7043b3b6d71a7902f50d22a26c SHA1: 4b8eca13f0b634e3835ca0741e93d4067ef7bc7c SHA256: a2d8c7e131b60cf3f8401382e9661bacbf3e345946fd29524bd6ab63dd0e1582 Section: science Priority: optional Homepage: http://wgs-assembler.sourceforge.net Description: Whole-Genome Shotgun Assembler Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celera Genomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008). Original-Maintainer: Sergey Koren Package: centrifuge Version: 1.0.4beta-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bowtie2, libparallel-forkmanager-perl Filename: ./centrifuge_1.0.4beta-1lbi_amd64.deb Size: 2664580 MD5sum: b91cb5e20a869b8d08110c9bdf40f1a2 SHA1: a0aa518a544cd7d37f7ec040d5b36dd71b09c201 SHA256: 1ac731da0af41074b5becb3bc73ee11286249dd7e19ab43d1493841321650ea7 Section: science Priority: optional Homepage: https://ccb.jhu.edu/software/centrifuge/ Description: Classifier for metagenomic sequences Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Original-Maintainer: Centrifuge Team Package: checkm-genome Version: 1.2.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: hmmer (>= 3.1b1), prodigal (>= 2.6.1), pplacer (>= 1.1), python3 (>= 3.6), python3-numpy (>= 1.13.1), python3-scipy (>= 0.19.1), python3-matplotlib (>= 2.1.0), python3-pysam (>= 0.12.0.1), python3-dendropy (>= 4.4.0) Filename: ./checkm-genome_1.2.0-1lbi_all.deb Size: 99968 MD5sum: e7015065309c0f403507ad58b5a7431b SHA1: 2acbe5aecb917fe84a61c7aa6b62ed5174ef9666 SHA256: 0ae7a9e5bdc0cd5aa8ba9c65ac3b803c7d43f13e7b5a5bd716b118cd286f2957 Section: science Priority: optional Homepage: https://ecogenomics.github.io/CheckM/ Description: Assess the quality of putative genome bins CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree. Original-Maintainer: Donovan Parks Package: checkv Version: 0.6.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: diamond-aligner (>= 0.9.22), hmmer (>= 3.1), ncbi-blast+ (>= 2.5.0), prodigal (>= 2.6.3), python3-biopython, python3-numpy, python3-psutil Filename: ./checkv_0.6.0-0lbi_all.deb Size: 561008 MD5sum: c3d22c038b3812e382bdc5369c379b68 SHA1: 6cf8d06607efcac2319ebc200a6a27dc0ae2c90b SHA256: 77c23d6abd74238ad9a2706339ccd6cfe16c9b4f16fb8d4560ace9692ff5adef Section: science Priority: optional Homepage: https://bitbucket.org/berkeleylab/checkv Description: Assess the quality of metagenome-assembled viral genomes CheckV is a fully automated command-line pipeline for assessing the quality of metagenome-assembled viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. Original-Maintainer: Katherine Pollard Package: chromosomer Version: 0.1.4a-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-bioformats, python-future, python-pyfaidx, python-pyvcf Filename: ./chromosomer_0.1.4a-1lbi_amd64.deb Size: 1392594 MD5sum: d695374673d6251ed84d56196ee3cd09 SHA1: b739e4de118a95f4c5a4b2c8da35c642ce805ed2 SHA256: a5a221f0fc98a1fb3f6777729670f8facf0ea93ab47e9bca06aecb6ec00da519 Section: science Priority: optional Homepage: https://github.com/gtamazian/chromosomer Description: A reference-assisted assembly tool Chromosomer is a reference-assisted assembly tool for producing draft chromosome sequences. Original-Maintainer: Gaik Tamazian Package: circexplorer Version: 1.1.10-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bedtools, python-pysam (>= 0.8.2), python-docopt, tophat (>= 2.0.9) Suggests: star (>= 2.4.0) Filename: ./circexplorer_1.1.10-0lbi_amd64.deb Size: 196912 MD5sum: 22a9041eef3ad5f700c0d4d30c19ac5b SHA1: b2009962a2fd2b1f8956d1d7f8914d6e79272502 SHA256: 430682aa612c014112e236ba14264816b9fa45874f5edfdd45a5418d5a48c0e7 Section: science Priority: optional Homepage: https://github.com/YangLab/CIRCexplorer Description: A combined strategy to identify circular RNAs CIRCexplorer is a combined strategy to identify junction reads from back spliced exons and intron lariats. . CIRCexplorer is now only a circular RNA annotating tool, and it parses fusion junction information from mapping results of other aligners. The result of circular RNA annotating is directly dependent on the mapping strategy of aligners. Different aligners may have different circular RNA annotations. CIRCexplorer is now only in charge of giving fusion junctions a correct gene annotation. Original-Maintainer: Xu-Kai Ma Package: ciri Version: 2.0.6-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Filename: ./ciri_2.0.6-0lbi_all.deb Size: 26572 MD5sum: 7dd68cea9b63379b36bbf23d37554cb6 SHA1: 64ba0f85a2f1f93ecffdfa2c506af728cac1ee4e SHA256: c1ea32bcea81dc4b098c7868d91730fa05170881d3e4822652b27f1a1cc27058 Section: science Priority: optional Homepage: https://sourceforge.net/projects/ciri/ Description: CircRNA Identifier. A de novo circular RNA identification tool CIRI (circRNA identifier) is a novel chiastic clipping signal based algorithm, which can unbiasedly and accurately detect circRNAs from transcriptome data by employing multiple filtration strategies. Original-Maintainer: Yuan Gao Package: clark Version: 1.2.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: openmpi-bin Filename: ./clark_1.2.3-0lbi_amd64.deb Size: 242836 MD5sum: 72439e28a9f9af35e3b6f25aabc03c40 SHA1: a0934adedb6dc7a1e95025be7ba93732ed5ea39f SHA256: 1115931a65b566b711c998d7c5a1e31dfbe8709a9001dcfd1cbcfc2f84ab907c Section: science Priority: optional Homepage: http://clark.cs.ucr.edu/ Description: CLAssifier based on Reduced K-mers CLARK (CLAssifier based on Reduced K-mers) is a novel method for supervised sequence classification based on discriminative k-mers. Somewhat unique among other metagenomic and genomic classification methods, CLARK provides a confidence score for its assignments which can be used in downstream analysis. Original-Maintainer: Rachid Ounit Package: clonalframeml Version: 1.25-5lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libgsl-dev | libgsl0-dev, libstdc++6 (>= 4.4.0) Recommends: r-base Filename: ./clonalframeml_1.25-5lbi_amd64.deb Size: 96486 MD5sum: dd65ff5ffde2c9f7ad90a0992f3c2315 SHA1: 6a45ebe4333589572d4f5011f0ca3d268455d716 SHA256: 65b92f108f85878280fd6f75162e6bbb00c3d5038a018e522c51675e73a08782 Section: science Priority: optional Homepage: https://github.com/xavierdidelot/clonalframeml Description: Efficient Inference of Recombination in Whole Bacterial Genomes ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There are three main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for recombination, an estimation of the key parameters of the recombination process, and a genomic map of where recombination took place for each branch of the phylogeny. . ClonalFrameML is a maximum likelihood implementation of the Bayesian software ClonalFrame. The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues. Original-Maintainer: Xavier Didelot , Daniel Wilson Package: concoct Version: 1.1.0-5lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bedtools, cython3 (>= 0.26.1), libgsl-dev, python3-bcbio-gff (>= 0.4), python3-biopython (>= 1.63), python3-nose (>= 1.3.0), python3-numpy (>= 1.8.0), python3-pandas (>= 0.13.0), python3-scipy (>= 0.13.3), python3-sklearn (>= 0.14.1), samtools Filename: ./concoct_1.1.0-5lbi_amd64.deb Size: 124224 MD5sum: 57b5e8b56c751b60fc805e781e2a5c00 SHA1: 314ef6dfc04a6b988ea4bffa2cbbb4f15a468076 SHA256: adcf1b2a3090ae564424b9b47699057cdbd1554a17e68cb09296067dd262bada Section: science Priority: optional Homepage: https://github.com/BinPro/CONCOCT Description: Clustering cONtigs with COverage and ComposiTion Concoct is a program that combines three types of information - sequence composition, coverage across multiple sample, and read-pair linkage - to automatically bin metagenomic contigs into genomes. Author: Brynjar Smari Bjarnason Original-Maintainer: Johannes Alneberg Package: constrains Version: 0.1.0-4lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7), python-biopython, python-numpy, python-scipy, python-networkx, bowtie2 (>= 2.2.1), metaphlan2 (>= 2.1) Filename: ./constrains_0.1.0-4lbi_all.deb Size: 35532 MD5sum: b36ac93968d9d280c7476b24548d450a SHA1: 1baefb739659b617e06b7d2913a87d5966f9f27c SHA256: 81ab435bd5d0894c05f7bf2d091051005abb53a138a4fcd8092da2355fa9a4cc Section: science Priority: optional Homepage: https://bitbucket.org/luo-chengwei/constrains Description: Identifying Conspecific Strains within metagenomic species ConStrains reconstructs the within-species diversity and SNP types by deconvoluting SNPs patterns across different conserved genes and across different samples. Original-Maintainer: Chengwei Luo Package: conterminator Version: 20200126-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./conterminator_20200126-1lbi_amd64.deb Size: 22201036 MD5sum: d47efc350694a99e8d49c97991d2fa6b SHA1: 4befc85e791f75966139afe9df4436475ab06346 SHA256: dc6bc1858d810c3f97bc872b276530132bc647c1d118c92dda60065428c1e4d7 Section: science Priority: optional Homepage: https://github.com/martin-steinegger/conterminator Description: Detection of incorrectly labeled sequences across kingdoms Conterminator is an efficient method to detect incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison. Original-Maintainer: Martin Steinegger Package: contiguator Version: 2.7.5-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: ncbi-blast+, python-biopython Recommends: abacas, mummer, perl, primer3 Suggests: artemis Filename: ./contiguator_2.7.5-0lbi_all.deb Size: 45432 MD5sum: 9b88137b4044d0d6d9aece1abe78827b SHA1: 6f897cbb3717985228f8acefbb9645cc68237233 SHA256: 6bab68d351642e869452f15d298be959848e11ec9fc196b0ab5f169f4d5fa76d Section: science Priority: optional Homepage: http://contiguator.sourceforge.net/ Description: Bacterial finishing tool for draft genomes CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome finshing process, taking advantage of the high number of near genomes that can be used to align and resolve the relative position of the contigs obtained with the latest sequencing technologies and therefore to design a set of PCR primers in order to fill the gaps and take a step further in the finishing process. It also can be used to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT). Original-Maintainer: Marco Galardini Package: coperead Version: 1.1.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: zlib1g-dev Filename: ./coperead_1.1.2-0lbi_amd64.deb Size: 450934 MD5sum: 3a734ef7ba118df86bffd236914362fb SHA1: 44957762a63b7725bdd7c50e8875a86bea90c544 SHA256: 4b45e6ee660da4d1a0f7f90b143fa6b65dc95d49c467b1196b96a96bd03acb73 Section: science Priority: optional Homepage: http://sourceforge.net/projects/coperead/ Description: Connecting Overlapped Pair-End Reads COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length. The connected reads can be used in genome assembly, resequencing and transcriptome research. Original-Maintainer: Binghang Liu , Jianying Yuan Package: cpat Version: 3.0.5-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3 (>= 3.5), python3-numpy, python3-pysam, r-base-core Filename: ./cpat_3.0.5-0lbi_all.deb Size: 5047956 MD5sum: 163b3a380664b8cb55aeb9228c10b45a SHA1: 0319b507f0aee8f83dbc24d6bd12e360ffbe01c6 SHA256: 5d9e20bfe670b86b2d1b125f0883641814741250eb15d4c5896bb966e7f5c5ee Section: science Priority: optional Homepage: https://cpat.readthedocs.io/en/latest/ Description: Coding Potential Assessment Tool CPAT is a bioinformatics tool to predict RNA's coding probability based on the RNA sequence characteristics. To achieve this goal, CPAT calculates scores of these 4 linguistic features from a set of known protein-coding genes and another set of non-coding genes: 1. ORF size 2. ORF coverage 3. Fickett TESTCODE 4. Hexamer usage bias CPAT then builds a logistic regression model using these 4 features as predictor variables and the "protein-coding status" as the response variable. After evaluating the performance and determining the probability cutoff, the model can be used to predict the coding potential of new RNA sequences. Original-Maintainer: Liguo Wang Package: cpc Version: 0.9-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: estate, libsvm-tools, ncbi-blast+ Filename: ./cpc_0.9-0lbi_all.deb Size: 115028 MD5sum: 71114b39ecdc73b26805c68f41b4a603 SHA1: 30382af801659ecf0b623841e3a4ccada280ccc8 SHA256: 65a9b08e7d8ceb9f27225643a1abfc9ff7e917157827e7c438dfef6d65ac94cc Section: science Priority: optional Homepage: http://cpc.cbi.pku.edu.cn/ Description: Coding Potential Calculator Coding Potential Calculator (CPC) is a Support Vector Machine-based classifier to assess the protein-coding potential of a transcript (i.e whether a cDNA/RNA transcript could encode a peptide or not) based on six biologically meaningful sequence features. It takes nucleotide FASTA sequences as input, and generate output about the coding status and the "supporting evidence" for the sequence. Original-Maintainer: CPC Team Package: cufflinks Version: 2.2.1+lbi-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libboost-serialization-dev, libboost-system-dev, libboost-thread-dev, libc6 (>= 2.23), libgcc1 (>= 1:4.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3), python2 Enhances: tophat Filename: ./cufflinks_2.2.1+lbi-2lbi_amd64.deb Size: 35329348 MD5sum: bb03244f8afceab9141d3094a4f5bf9e SHA1: c512da6fc4453c6bc2a8880b1f398fd24d948728 SHA256: 10450f7c40f4e10934cd4554074ceb71277a75033d017632179b81a5f004fb67 Section: non-free/science Priority: optional Homepage: http://cufflinks.cbcb.umd.edu Description: Transcript assembly, differential expression and regulation for RNA-Seq Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. Original-Maintainer: Debian Med Packaging Team Package: cutadapt Version: 1.12-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python-xopen Conflicts: python-cutadapt Replaces: python-cutadapt Filename: ./cutadapt_1.12-2lbi_all.deb Size: 435116 MD5sum: a90ff8bfacb2d906e60b179494e54a71 SHA1: 10a6170af83088bf2eaf6dfee98920433aaa1f22 SHA256: db6a0c2eacdf5bd80c71c86aff44079a848a05dfa8e4166a12a22f991406195e Section: science Priority: optional Homepage: https://cutadapt.readthedocs.org/ Description: trim adapters from high-throughput sequencing reads Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. . Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but often you don’t want them to be in your reads. . Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all. Original-Maintainer: Marcel Martin Package: das-tool Version: 1.1.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: ncbi-blast+ (>= 2.2.31), prodigal (>= 2.6.3), pullseq (>= 1.0.2), r-base-core (>= 3.2.3), r-cran-data.table (>= 1.9.6), r-cran-domc (>= 1.3.4), r-cran-ggplot2 (>= 2.1.0), ruby (>= 2.3.0) Filename: ./das-tool_1.1.0-0lbi_all.deb Size: 37338378 MD5sum: 0259ed102372238672643dd373a878c0 SHA1: 140f89f27626dbed77c6b7cbe60d37212dfba2c8 SHA256: 3defe4160fa2f0296e96a43f30deeabbc2da70194bb0908258b9732b12d4fec8 Section: science Priority: optional Homepage: https://github.com/cmks/DAS_Tool Description: DAS Tool for genome resolved metagenomics DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Original-Maintainer: Christian M K Sieber Package: deeptools Version: 3.0.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3, python3-matplotlib (>= 1.5.1), python3-numpy (>= 1.9.0), python3-numpydoc (>= 0.5), python3-plotly (>= 1.9.0), python3-py2bit (>= 0.1.0), python3-pybigwig (>= 0.2.1), python3-pysam (>= 0.14), python3-scipy (>= 0.17.0) Filename: ./deeptools_3.0.1-0lbi_amd64.deb Size: 211232 MD5sum: 9bbbfbe293c8687d800ddd850766672b SHA1: 54e631fc4c78c16a9567f1838c2f508347586ba8 SHA256: dd06fc5a5ed33232506f56c950846b5dce07f89851e20e7ddc192526364f85ce Section: science Priority: optional Homepage: https://deeptools.readthedocs.io/ Description: Tools for exploring deep sequencing data deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Original-Maintainer: Fidel Ramirez Package: defense-predictor Version: 0.1.2-9lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3 (>= 3.10), python3-fair-esm (>= 2.0.0), python3-joblib (>= 1.4.2), python3-numpy (>= 2.1.2), python3-pandas (>= 2.2.3), python3-lightgbm (>= 4.5.0), python3-sklearn (>= 1.5.2), python3-torch (>= 2.5.1), python3-torch (<= 2.6.0), python3-tqdm (>= 4.67.0), python3-requests (>= 2.32.3) Filename: ./defense-predictor_0.1.2-9lbi_all.deb Size: 18278 MD5sum: 6c5444e322dc07b291c4212f3de89a09 SHA1: c5f7ac8c7c4e6e709a3aaa54ee5484c7c5d8e162 SHA256: e1c2529c406bf91749e6d14387f798a974582a74244a5daf1c94799e2a931ae8 Section: science Priority: optional Homepage: https://github.com/PeterDeWeirdt/defense_predictor Description: A ML model to predict antiphage defense systems Python package to run DefensePredictor, a machine-learning model that leverages embeddings from a protein language model, ESM2, to classify proteins as anti-phage defensive. Original-Maintainer: Peter DeWeirdt Package: dekupl-run Version: 1.0-3lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: cmake, jellyfish, kallisto, pigz, python3-rpy2, r-bioc-deseq2, r-cran-pheatmap, r-cran-rcolorbrewer, snakemake Filename: ./dekupl-run_1.0-3lbi_all.deb Size: 14638562 MD5sum: 13891d10c9835f84d29cfabc9252be82 SHA1: a88e26aea5aa9301958e36aa728d70b5372370e2 SHA256: 345ef2811b071b46316d450aa7afe077b16a4b5d10381db7677f3b0707fea21b Section: science Priority: optional Homepage: https://github.com/Transipedia/dekupl-run Description: Identify differentially expressed k-mers between RNA-Seq datasets DE-kupl is a pipeline that finds differentially expressed k-mers between RNA-Seq datasets. Dekupl-run handles the first part of the DE-kupl pipeline (https://github.com/Transipedia/dekupl) from raw FASTQ to the production of contigs from differentially expressed k-mers. Original-Maintainer: Jérôme Audoux Package: diamond-aligner Version: 2.0.15-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: zlib1g-dev Filename: ./diamond-aligner_2.0.15-0lbi_amd64.deb Size: 9844558 MD5sum: 238c4226b6dc3f6106e60f18a93fde28 SHA1: 23e8b772e2e6b17c3095f274bd4ca5c4ab697b8c SHA256: cae6e0599ebecbb66dd7cccb3e2d191e86055cbd580f5775750d77b12dcc5870 Section: science Priority: optional Homepage: http://github.com/bbuchfink/diamond Description: BLAST-compatible local aligner DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. Original-Maintainer: Benjamin Buchfink Package: dips Version: 1.0.6-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python-jinja2, python-levenshtein, python-nose Filename: ./dips_1.0.6-0lbi_all.deb Size: 12489576 MD5sum: 175576b5b81ce1ffab57c8659ccf0b00 SHA1: 766826b0d320e64f9907dd2034e96e070e022d3c SHA256: 556a21ef1d32d3f349fa924a9032cea0ca3df3b56e7c60e7ec597f5670c226ab Section: science Priority: optional Homepage: https://bitbucket.org/incpm/dips Description: pTA - Peptide Tag Assembler Original-Maintainer: Ophir Tal , Rotem Barzilay Package: discovardenovo Version: 52488-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libjemalloc-dev, samtools Recommends: graphviz, picard-tools Filename: ./discovardenovo_52488-0lbi_amd64.deb Size: 241945372 MD5sum: 0110170fa1eb9b833139b71ef1e2e5b1 SHA1: be751f8ede5df0d21b723ef11059382c6c938e58 SHA256: cd3f99cd2705b01579a9f506563db83c743f1bd34e0b7b6b63fbeb55ff28ed7c Section: science Priority: optional Homepage: https://software.broadinstitute.org/software/discovar/blog/ Description: DISCOVAR de novo genome assembler DISCOVAR de novo is a large (and small) de novo genome assembler. It quickly generates highly accurate and complete assemblies using the same single library data as used by DISCOVAR. It currently doesn’t support variant calling – for that, please use DISCOVAR instead. Original-Maintainer: Neil Weisenfeld Package: drep Version: 1.4.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: mash (>= 1.1.1), mummer (>> 3.22), python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pytest, python3-seaborn, python3-sklearn Recommends: checkm-genome (>= 1.0.6), prodigal (>= 2.6.3) Suggests: centrifuge Filename: ./drep_1.4.3-0lbi_amd64.deb Size: 79264 MD5sum: aa40fb23e1556aff63fe41bcd2a2bded SHA1: 7ff20a3e6d592f7332a20d940f730fccaa53b5ff SHA256: 1bba5985a51bc99f2ba0eb412bf5e1a6bc9c550a5f8db247e0c887d54b04d241 Section: science Priority: optional Homepage: https://github.com/MrOlm/drep Description: De-replication of microbial genomes dRep is a program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set. Author-Email: mattolm@berkeley.edu Original-Maintainer: Matt Olm Package: eagler Version: 1.0.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bwa (>= 0.7.12), libseqan2-dev Recommends: python3 Filename: ./eagler_1.0.1-0lbi_amd64.deb Size: 628284 MD5sum: 4f0afad86c5851baeb731d229341a24d SHA1: 95753410545efde2ca4232b93d2f5782eadc66e8 SHA256: 1f790e2f360540bdfad66d13f085f067a4a00ceb3295ec403b98a924e7a611af Section: science Priority: optional Homepage: https://github.com/mculinovic/EAGLER Description: Eliminating Assembly Gaps by Long read Extension EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads. Original-Maintainer: Marko Culinovic , Luka Sterbic Package: eggnog-mapper Version: 2.1.12-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3, python3-biopython (>= 1.76), python3-psutil (>= 5.7.0), python3-xlsxwriter (>= 1.4.3) Filename: ./eggnog-mapper_2.1.12-2lbi_all.deb Size: 29718846 MD5sum: f8a009ff32d69558c64e15d32287ef3f SHA1: b7c03b0d7c7f19a4c591e6e703e7c6acc1f1da4b SHA256: 8228c93da472e74a23d8315319c1de5864536d94cc4ccfb80faf2b40663a536e Section: science Priority: optional Homepage: https://github.com/eggnogdb/eggnog-mapper Description: Fast genome-wide functional annotation through orthology assignment EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. . Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. . The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence). Original-Maintainer: Jaime Huerta-Cepas , Peter Bork Package: elsa Version: 1.0.2-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libstdc++6, python2.7, python-biopython, python-matplotlib (>= 0.98), python-numpy (>= 1.0), python-scipy (>= 0.6) Filename: ./elsa_1.0.2-1lbi_amd64.deb Size: 562232 MD5sum: 948e19c276de27a81ea1730228fec1a9 SHA1: 8cf846b96ab9e2966371264b77debb0c49291996 SHA256: 42d7b0f2a9cac2b68a92bb850b4b15a2c631f00259e39e430b6a0ac8823e84f2 Section: science Priority: optional Homepage: http://bitbucket.org/charade/elsa Description: ELSA: Extended Local Similarity Analysis This python module provide tools for aligning and analyzing the time shift dependent pairwise correlation between two sequence of evenly spaced observation data. Permutation test is used to estimate the P-value. The results can be summarized and easily queried for desired analysis. Original-Maintainer: Li Charlie Xia Package: enrichm Version: 0.5.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: diamond-aligner (>= 0.9.22), hmmer (>= 3.1b), mcl (>= 14-137), mmseqs2 (>= 2-23394), parallel (>= 20161222), prodigal (>= 2.6.3), python3 (>= 3.6), python3-biopython (>= 1.66), python3-dateutil (>= 2.5.1), python3-numpy (>= 1.9.1), python3-pandas (>= 0.17.0), python3-scipy (>= 0.17.0), python3-six (>= 1.10.0), python3-sklearn, python3-statsmodels (>= 0.8.0rc1), seqmagick (>= 0.6.1), r-base-core (>= 3.0.1), r-cran-gridextra, r-cran-optparse Recommends: python3-levenshtein Filename: ./enrichm_0.5.0-1lbi_all.deb Size: 113968 MD5sum: 4b4038dfda22b81d9f0faa986ed8f35f SHA1: 8084d0771cfe7ad40e37832b1c889315d10d9bca SHA256: 42dcadbfedac6b61aad78205f94298f0beaa7d184301cd51d9bcdba680c0dcd3 Section: science Priority: optional Homepage: https://github.com/geronimp/enrichM Description: Toolbox for comparing the functional composition of population genomes EnrichM is a set of comparative genomics tools for large sets of metagenome assembled genomes (MAGs). Original-Maintainer: Joel Boyd Package: estate Version: 0.5.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./estate_0.5.0-0lbi_amd64.deb Size: 121324 MD5sum: ba5a34da26564d397afada2a4580df11 SHA1: 43b65d4d1f1ff6334f1c0ca4548b0c866af212b2 SHA256: 0c8fe0113882d9e12668852c658753b85991aa2a2ec6c255a564868fbc278c85 Section: science Priority: optional Homepage: http://www.hgmp.mrc.ac.uk/~gslater/ESTate/ Description: Expressed Sequence Tag Analysis Tools, etc ESTate is a set of tools for Expressed Sequence Tag Analysis etc. Designed to perform a number of tasks required in the analysis of ESTs, such as sequence comparison, database searching, clustering, and translation. Original-Maintainer: Guy St.C. Slater Package: fastani Version: 1.33-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libboost-dev | libgsl-dev, zlib1g Filename: ./fastani_1.33-0lbi_amd64.deb Size: 2009540 MD5sum: 5fad239d56dce0b8493bab78fb11073c SHA1: cb2678519305fe641c059bede78bb588a97c7b50 SHA256: 7089e1c79d7b67bc7e8387c18516b13180d1dfe8749d3c613c45f1b24841477e Section: science Priority: optional Homepage: https://github.com/ParBLiSS/FastANI Description: Fast Whole-Genome Similarity (ANI) Estimation FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Original-Maintainer: Chirag Jain Package: fastp Version: 0.18.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./fastp_0.18.0-0lbi_amd64.deb Size: 1321018 MD5sum: 2ab434dea8adf200ac4c3594ab1dbd96 SHA1: c3a75fdee1e0100130da3f9c81704d5c0b58d229 SHA256: 67bff5546d572a3629ad354e101a830a008e85b2eb46ffb1289f34de21b4ea0b Section: science Priority: optional Homepage: https://github.com/OpenGene/fastp Description: An ultra-fast all-in-one FASTQ preprocessor A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Original-Maintainer: Shifu Chen Package: fastqc Version: 0.11.8-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: libcommons-math3-java, libjbzip2-java, libhtsjdk-java, default-jre Filename: ./fastqc_0.11.8-0lbi_all.deb Size: 9740720 MD5sum: 3dc1eac1dcea1178507ce62f1009e126 SHA1: 91174dc2fc7869879d300f42ef18722057318d9a SHA256: 60b3451e517acd00f61316712820a86c2bd69b5b77c347a806fb8db4a175e6c1 Section: science Priority: optional Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Description: quality control for high throughput sequence data FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. . The main functions of FastQC are * Import of data from BAM, SAM or FastQ files (any variant) * Providing a quick overview to tell you in which areas there may be problems * Summary graphs and tables to quickly assess your data * Export of results to an HTML based permanent report * Offline operation to allow automated generation of reports without running the interactive application Package: fastx-toolkit Version: 0.0.14-5 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 564 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libgtextutils0v5, libstdc++6 (>= 5.2), libgd-graph-perl, libperlio-gzip-perl Filename: ./third-party/fastx-toolkit_0.0.14-5_amd64.deb Size: 115892 MD5sum: 65b671aa151229e78f98ad8739ff9c66 SHA1: 12a5f5934791383d7f9d3859820e23859a0ce13f SHA256: 1e58ec9e82f0b7be422939c042294d25096ecdeb669bd38516b1785baf980407 Section: science Priority: optional Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Description: FASTQ/A short nucleotide reads pre-processing tools The FASTX-Toolkit is a collection of command line tools for preprocessing short nucleotide reads in FASTA and FASTQ formats, usually produced by Next-Generation sequencing machines. The main processing of such FASTA/FASTQ files is mapping (aligning) the sequences to reference genomes or other databases using specialized programs like BWA, Bowtie and many others. However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome—manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks. . (Repackaged on Mon, 02 May 2022 16:16:08 -0300 by dpkg-repack.) Package: find-circ Version: 1.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bowtie2, python-pysam, samtools Filename: ./find-circ_1.2-0lbi_amd64.deb Size: 203190 MD5sum: 6cdc6ae60e4c7f01faa42bdd8bd31ea1 SHA1: 9bb77ef59fab2ffb459f5467fac6cf8ba05c335b SHA256: 7711883c78ad97e84c34fe63e3fd81b08f81857a7b1084e4e2493759b7f03a4e Section: science Priority: optional Homepage: https://github.com/marvin-jens/find_circ/ Description: Tools to find circRNAs in RNA-seq data This software detects head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data. It is also used extensively by circbase. Original-Maintainer: Nikolaus Rajewsky Package: fraggenescan Version: 1.19-1lbi Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 6545 Depends: libc6 (>= 2.14), python2 Filename: ./fraggenescan_1.19-1lbi_amd64.deb Size: 1271904 MD5sum: 1bcbf4631db024b0f54a670bfce968d6 SHA1: 4aa58c94578cc0d9e89c123998395c209636a9c0 SHA256: cec37b4c4baf3534d650e9f9cb4dfd1e244f93abf92536091797c9655d126535 Section: science Priority: optional Homepage: http://sourceforge.net/projects/fraggenescan/ Description: finds (fragmented) genes in short reads FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. . This package installs the run_FragGeneScan.pl script as /usr/bin/fraggenescan and it does not need to be run from any particular directory. Package: gapfiller Version: 2.1.2-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Filename: ./gapfiller_2.1.2-0lbi_all.deb Size: 225920 MD5sum: 1932249751cecce3517b1cb4a74f5cdc SHA1: 77dd7e4f6cc745da09b93236844835e6e875e9bb SHA256: bbb9cd3a4aa43fee3c7d2a624b15d3016c8a7ca8217caa1406310c1c4e07e7b8 Section: science Priority: optional Homepage: https://sourceforge.net/projects/gapfiller/ Description: A de novo local assembler for paired reads. GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. A set of coupled reads (seeds) is required, as well as a set of reads to fill the gap between the two mates. The only restriction on the reads library is that seeds are inner oriented (paired-reads) or outer oriented (mate-pairs). Insert size refers to the largest distance between the seeds. GapFiller works better on short inserts (i.e., less than 1 kbp), however in principle it can be used to assemble larger ones (i.e., mate-pairs inserts). GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. Original-Maintainer: Francesca Nadalin Package: gatk Version: 4.1.2.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: openjdk-8-jre, python2 (>= 2.6), python3 (>= 3.6.2), r-base (>= 3.2.5) Filename: ./gatk_4.1.2.0-1lbi_all.deb Size: 383841540 MD5sum: 5413db555b8676c36f76efdf523dc729 SHA1: ecdaf37e7d1bf121e822da15fe91ba1d0cdbffb3 SHA256: a0031a57755ae1be6deed6121c005fbcb457ada388bfb8b32a9419daacdad089 Section: science Priority: optional Homepage: https://software.broadinstitute.org/gatk/ Description: Variant Discovery in High-Throughput Sequencing Data Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Original-Maintainer: Louis Bergelson Package: gdc-data-transfer Version: 2.3.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Conflicts: genetorrent-download Filename: ./gdc-data-transfer_2.3.0-0lbi_amd64.deb Size: 22705512 MD5sum: fe35361be45e16eb80682aa52b30a013 SHA1: 63b1c9325c0728563370d2b900d31ccce1fcf3d7 SHA256: b0a3aecbebf9d80a3a3ec74e167f53a562ea8c905394717aeb17ab781fc45164 Section: science Priority: optional Homepage: https://gdc.nci.nih.gov/node/159/ Description: GDC Data Transfer Tool The GDC provides a standard client-based mechanism in support of high performance data downloads and submission. . The raw sequence files, typically stored as BAM or FASTQ, make up the bulk of data. The size for a single file can vary greatly depending on the specific analysis; However, some of the whole genome BAM files in The Cancer Genome Atlas (TCGA) reach sizes of 200-300 GB. In such cases, a high performance data download and submission client is essential. Original-Maintainer: GDC Help Desk Package: gdrive Version: 2.1.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./gdrive_2.1.0-0lbi_amd64.deb Size: 1862440 MD5sum: 239a180482f607cb8b290111002274fe SHA1: 944c4475dd990bc17aa0fa40d684a1f603eda0f8 SHA256: 61c9f146c4bc31fa9f19c577bf785cac26485f2b4ca27e393387df979cfcc982 Section: science Priority: optional Homepage: https://github.com/gdrive-org/gdrive Description: Google Drive CLI Client gdrive is a command line utility for interacting with Google Drive Original-Maintainer: Petter Rasmussen Package: genomicconsensus Version: 1.1.0-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: dh-python, libboost-dev, python2 (>= 2.7.3), python2 (<< 3), python-consensuscore, python-functools32, python-h5py (>= 2.0.1), python-iso8601, python-jsonschema, python-numpy (>= 1.6.0), python-pbcommand (>= 0.2.0), python-pbcore (>= 1.2.2) Provides: quiver Filename: ./genomicconsensus_1.1.0-2lbi_amd64.deb Size: 89004 MD5sum: 1b1471b0535858a96944a7dbc55a057a SHA1: ebe4be13a29f066910c9256a56ac66166fb80565 SHA256: 6ba1f1ae3726b6ce329c280d7f24ebb100584c56cd7018829707810369e721e5 Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/GenomicConsensus Description: Provides the quiver tool Quiver is an algorithm for calling highly accurate consensus from multiple PacBio reads, using a pair-HMM exploiting both the basecalls and QV metrics to infer the true underlying DNA sequence. Original-Maintainer: Pacific Biosciences Package: glimmer3 Version: 3.02-4biolinux2.1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 881 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0) Recommends: tcsh | csh Conflicts: tigr-glimmer Replaces: tigr-glimmer Provides: glimmer, tigr-glimmer Filename: ./glimmer3_3.02-4biolinux2.1_amd64.deb Size: 280812 MD5sum: 85b1d81529b1d31cdb46259640f93007 SHA1: 5dbd9ee78a5d4a16596210bb0b941b1dbefba7dc SHA256: 835a8626e87f527107287b58b609e1e0611abd36fa1571bb0249f65a98034e5e Section: science Priority: optional Homepage: http://www.cbcb.umd.edu/software/glimmer Description: Gene detection in archea and bacteria Developed by the JHU CCB this software detects coding sequences in bacteria and archea. . Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Package: groopm Version: 2.0.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-bamm, python3-imageio (>= 2.2.0), python3-matplotlib (>= 1.1.0), python3-numpy (>= 1.6.1), python3-pandas (>= 0.23.3), python3-pil (>= 1.1.7), python3-scipy (>= 0.15.0), python3-sklearn, python3-tables (>= 2.3) Filename: ./groopm_2.0.0-1lbi_all.deb Size: 102052 MD5sum: a33d5c878226bb9e445cbc25706f9a80 SHA1: 9e0a7a426becee4427c058b204a581d3cfcbec18 SHA256: b4c7d203315c81fd974929496d3ccd5e578696f2f69642e90758b0639feb1f22 Section: science Priority: optional Homepage: http://pypi.python.org/pypi/GroopM/ Description: Metagenomic binning suite GroopM is a metagenomic binning toolset. It leverages spatio-temoral dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets. GroopM is largely parameter-free. Use: groopm -h for more info. Original-Maintainer: Michael Imelfort Package: gtdb-tk Version: 2.1.1-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: fastani (>= 1.32), fasttree (>= 2.1.9), hmmer (>= 3.1), libgomp1, libgsl-dev, libgslcblas0, mash (>= 2.2), pplacer (>= 1.1), prodigal (>= 2.6.2), python3 (>= 3.6), python3-dendropy (>= 4.1.0), python3-numpy (>= 1.9.0), python3-tqdm (>= 4.35.0) Filename: ./gtdb-tk_2.1.1-0lbi_all.deb Size: 122220 MD5sum: 1e509cbf404a75ce562f0ece90833599 SHA1: 86e362da20d126c5c5e1631ecced1f87d59e10e2 SHA256: 0ef9a2ccfcf802fe93637a1452de2bbfa92659256b4336f8d52c526fbf0ff2df Section: science Priority: optional Homepage: https://github.com/Ecogenomics/GTDBTk Description: Objective taxonomic classifications to bacterial and archaeal genomes GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy [GTDB] (https://gtdb.ecogenomic.org/). It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. Original-Maintainer: Pierre-Alain Chaumeil , Donovan Parks Package: humann2 Version: 2.8.1-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bowtie2 (>= 2.1), diamond-aligner (>= 0.8.22), glpk-utils, metaphlan2 (>= 2.6), python2 (>= 2.7), python2 (<< 3) Filename: ./humann2_2.8.1-2lbi_amd64.deb Size: 5358608 MD5sum: 317793c5f47e7a786b8d3ea19d9a0b68 SHA1: c5929c3f3e6d2efd154613160fd46a87bde8a75f SHA256: 4c49e1c192379a90a7df121374cf78d443ea47d271a30c4511ff9cf0bcb0ad09 Section: science Priority: optional Homepage: http://huttenhower.sph.harvard.edu/humann2 Description: The HMP Unified Metabolic Analysis Network 2 HUMAnN2 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question: What are the microbes in my community-of-interest doing (or capable of doing)? Original-Maintainer: HUMAnN2 Development Team , Lauren McIver Package: hyphy Version: 2.1+20111219-6biolinux1.1 Architecture: amd64 Maintainer: Tim Booth , H. Soon Gweon Installed-Size: 6845 Depends: libc6 (>= 2.14), libcurl3-gnutls (>= 7.16.2), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.1.1) Filename: ./hyphy_2.1+20111219-6biolinux1.1_amd64.deb Size: 1533660 MD5sum: 5db4de29fab8fe6a2778b50a2463676d SHA1: 131bdca3947aad7e6501f3478c33b5a3fac13413 SHA256: c988f8405b0fbf14e116e9d82d903d44d57382999e7f61d867b4c9a61368ec19 Section: science Priority: extra Homepage: https://github.com/veg/hyphy/downloads Description: analysis of genetic sequences using multiple techniques HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. HyPhy has over 6500 registered users and has been cited in over 600 peer-reviewed publications (Google Scholar). Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939 Package: idba Version: 1.1.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./idba_1.1.3-0lbi_amd64.deb Size: 17659196 MD5sum: 34df353c222dfd11d12bfe36cdcb765c SHA1: 4dd88527d7196db84672cda7c221d23112e81a65 SHA256: 1e936569a128f351505491ec79ed96c6222a83520e3c8fa7b9644d5ad2c2c3b8 Section: science Priority: optional Homepage: https://github.com/loneknightpy/idba Description: De Bruijn Graph De Novo Assembler for Short Reads IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data. Original-Maintainer: Yu Peng Package: iqtree Version: 1.6.6-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./iqtree_1.6.6-0lbi_amd64.deb Size: 3223794 MD5sum: 2206268bccb7768252660faed39019fb SHA1: 39bafde64eadb71015289e28d9d65bda174baa34 SHA256: 6f3a8f491a3bc219f27f2f50a7596dfab2431f802573899121ab0a5db2680292 Section: science Priority: optional Homepage: http://www.iqtree.org/ Description: Efficient software for phylogenomic inference IQ-TREE is an efficient program for reconstructing large maximum likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. IQ-TREE extends the IQPNNI algorithm with many enhancements. Original-Maintainer: Heiko A. Schmidt Package: islandpath Version: 1.0.6-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: hmmer, libbio-perl-perl, libbio-procedural-perl, libconfig-simple-perl, liblog-log4perl-perl, libmoose-perl, libmoosex-singleton-perl, perl (>= 5.18), perl-doc Filename: ./islandpath_1.0.6-2lbi_all.deb Size: 3939452 MD5sum: 7f039e981a8b75bd40c0c18bb7a62526 SHA1: 2f92f77ef8d7ee9ff2d355f81b2cdac22b8cc2ec SHA256: b0cae68dbe03908fe2bbecf7a3abb3c10af24d5d93ce818e8d8dde64364f30e4 Section: science Priority: optional Homepage: https://github.com/brinkmanlab/islandpath Description: Predict genomic islands IslandPath-DIMOB is a standalone software to predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes. . Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest. . The latest IslandPath-DIMOB version is integrated in IslandViewer 4 (http://www.pathogenomics.sfu.ca/islandviewer/browse/), the leading integrated web interface for genomic island prediction. Original-Maintainer: Claire Bertelli Package: jellyfish1 Version: 1.1.11-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./jellyfish1_1.1.11-2lbi_amd64.deb Size: 1422558 MD5sum: 43ac6b2287ecb5f7c50bfa841e9cf72b SHA1: 18f65dc9bdd3cb70246d83e1f9267e004c5f4a60 SHA256: 0cbf8b6016077b5a516a2522bb5b554aee9962e540768150d1c74bde11c8817c Section: science Priority: optional Homepage: http://www.cbcb.umd.edu/software/jellyfish/ Description: Fast, Parallel k-mer Counting for DNA Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . This is the old version 1, for compatibility. It is recommended to use a newer version. Original-Maintainer: Guillaume Marcais , Carl Kingsford Package: k8 Version: 0.2.5-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libv8-dev, zlib1g Filename: ./k8_0.2.5-0lbi_amd64.deb Size: 1419930 MD5sum: 6022104e4a39742d004c4bf2bdbf89b1 SHA1: 3c6191d73b44a163b35f33958ecc6ca44290f73e SHA256: 80b4747fbd4721457776e088c6aef92b9135557af2e29e12007f6a0aea65a02b Section: science Priority: optional Homepage: https://github.com/attractivechaos/k8 Description: k8 Javascript shell K8 is a Javascript shell based on Google's V8 Javascript engine. It adds the support of flexible byte arrays and file I/O. Original-Maintainer: Heng Li Package: kma Version: 1.2.22-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libz-dev Filename: ./kma_1.2.22-0lbi_amd64.deb Size: 506884 MD5sum: 130b485929c32cfbcb1e68c9a88af9e3 SHA1: 6af690d050a59995404850c30c67430d9cd84fb1 SHA256: 6ba58a68cf2dfb3ffcf0b3abf38de85e42d4e04eaced845b103a760427d6026e Section: science Priority: optional Homepage: https://bitbucket.org/genomicepidemiology/kma/ Description: k-mer alignment - KMA KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. KMA is particulary good at aligning high quality reads against highly redundant databases, where unique matches often does not exist. It works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on our users demands. . If you use KMA for your published research, then please cite: Philip T.L.C. Clausen, Frank M. Aarestrup & Ole Lund, "Rapid and precise alignment of raw reads against redundant databases with KMA", BMC Bioinformatics, 2018;19:307. Original-Maintainer: Philip T.L.C. Clausen Package: kraken Version: 1.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: jellyfish1, libc6, libgcc1, libgomp1, libstdc++6, perl Filename: ./kraken_1.0-0lbi_amd64.deb Size: 104686 MD5sum: 63a0f20c30d4c892259058e09c7a5696 SHA1: f1bafd53b58f46bc170f8962a4da8595963ad3d6 SHA256: 6a5e8c7364dbd97fd87e987a2346050c8d54d74c993bd57364a5030e249b2456 Section: science Priority: optional Homepage: http://ccb.jhu.edu/software/kraken/ Description: Taxonomic Sequence Classification System Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Original-Maintainer: Derrick Wood Package: kraken2 Version: 2.0.6-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: jellyfish1, libc6, libgcc1, libgomp1, libstdc++6, perl Filename: ./kraken2_2.0.6-2lbi_amd64.deb Size: 109612 MD5sum: 40aa388c99672198f8765cbb303d0e85 SHA1: aa3627e31fad51d084049f7c924a184728c0c41b SHA256: 6325e899810521864b822877545f1d251af22958310082cb407e902abb314258 Section: science Priority: optional Homepage: http://ccb.jhu.edu/software/kraken/ Description: Taxonomic Sequence Classification System Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Original-Maintainer: Derrick Wood Package: krakenuniq Version: 0.7.3-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: jellyfish1, perl Filename: ./krakenuniq_0.7.3-1lbi_amd64.deb Size: 291564 MD5sum: 6955c948fa907db652a68ed169fd2a72 SHA1: 7e3a8ae3754236247fa1d66c016b351003c6ab94 SHA256: 3dca5daad3874c4745f7e0f4398d70441a881ab5c293514697e9067e336f13c7 Section: science Priority: optional Homepage: http://ccb.jhu.edu/software/kraken/ Description: Confident and fast metagenomics classification using unique k-mer counts False-positive identifications are a significant problem in metagenomics classification. KrakenUniq (formerly KrakenHLL) is a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. Original-Maintainer: Derrick Wood Package: kronatools Version: 2.8-6lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: curl, perl Conflicts: krona Replaces: krona Provides: krona Filename: ./kronatools_2.8-6lbi_all.deb Size: 145700 MD5sum: 94f8b458b41fb1401d89be9cc7672d27 SHA1: 7a1d240536bbea855f717e8c6814337d619fcacd SHA256: 56e138ea041853fff27e3dbeeb7b1ef842d9e64727ae1ea874bef1fd1adcf48c Section: science Priority: optional Homepage: https://github.com/marbl/Krona/wiki Description: Interactively explore metagenomes and more from a web browser Krona is a flexible tool for exploring the relative proportions of hierarchical data, such as metagenomic classifications, using a radial, space-filling display. It is implemented using HTML5 and JavaScript, allowing charts to be explored locally or served over the Internet, requiring only a current version of any major web browser. Krona charts can be created using an Excel template or from common bioinformatic formats using the provided conversion scripts. Original-Maintainer: Brian Ondov , Todd Harrington Package: ksnp Version: 3.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: fasttree, jellyfish, mummer, tcsh Filename: ./ksnp_3.1-0lbi_amd64.deb Size: 115895736 MD5sum: 2909c12bc14f8f568f5bc0065332bb09 SHA1: 00b22af4113025e270442a692398a44fc0b21eaf SHA256: 939cd4ea325c7d6fabacd998da87f4f7a0b2cb75867b0d1cd7f62b0588ad4be7 Section: science Priority: optional Homepage: https://sourceforge.net/projects/ksnp/ Description: SNP discovery and SNP annotation from whole genomes kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. Original-Maintainer: Barry Hall , Shea Gardner Package: libbio-db-eutilities-perl Version: 1.73-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: bioperl, libwww-perl, liburi-perl, libxml-simple-perl Filename: ./libbio-db-eutilities-perl_1.73-0lbi_all.deb Size: 62554 MD5sum: ae265071b6d3c9cbff235a1161f3c707 SHA1: 411a67e30b5a645a136366cd1f93b0dba8b72b7f SHA256: 358bc9b113cf42004e0db476142c06659b14387e540c78d9f11185fc02e1ee64 Section: science Priority: optional Homepage: https://metacpan.org/release/Bio-EUtilities Description: Webagent which communicates with NCBI's eUtils Webagent which interacts with and retrieves data from NCBI's eUtils. Original-Maintainer: Chris Fields Package: libbio-phylo-perl Version: 2.0.1-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: perl (>= 5.8.0), r-cran-phytools Filename: ./libbio-phylo-perl_2.0.1-0lbi_all.deb Size: 580712 MD5sum: 3d81224427c507567f017b57d009a340 SHA1: 7849f7647813c00693a2aafe22e16f6d6242543c SHA256: 6e9c5f92b702ba96309f49d0055c68c802389d85d9f486f3169c478e1892a350 Section: science Priority: optional Homepage: https://github.com/rvosa/bio-phylo Description: A toolkit for analyzing and manipulating phyloinformatic data Phylogenetics is the branch of evolutionary biology that deals with reconstructing and analyzing the tree of life. This distribution provides objects and methods to aid in handling and analyzing phylogenetic data. Original-Maintainer: Rutger Vos Package: libforkwork-ocaml Version: 0.3.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: ocaml-nox Filename: ./libforkwork-ocaml_0.3.2-0lbi_amd64.deb Size: 55720 MD5sum: adc3dd9d75a13a93720f03b5a77e74f7 SHA1: 6106f880170f2e013f5daee453071d1635503511 SHA256: c96a231630a491c0ddd4dfaf444107fa1f8add7960115a65001772dc1d9f52ff Section: science Priority: optional Homepage: https://github.com/mlin/forkwork Description: Fork child processes to perform work on multiple cores A simple OCaml library for forking child processes to perform work on multiple cores. ForkWork is intended for workloads that a master process can partition into independent jobs, each of which will typically take a while to execute (several seconds, or more). Also, the resulting values should not be too massive, since they must be marshalled for transmission back to the master process. Among the numerous tools for multicore parallelism available in the OCaml ecosystem, ForkWork fits somewhere in between Netmcore and Parmap. It's a bit easier to use than the former, and a bit more flexible than the latter. Original-Maintainer: Mike Lin Package: libgd-graph-histogram-perl Version: 1.1-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: perl Filename: ./libgd-graph-histogram-perl_1.1-1lbi_all.deb Size: 14252 MD5sum: 8361e0c923c2a88045458b2604a21597 SHA1: 4690deb0cf6888419c447599d14a60f64b01e107 SHA256: 69a63c451091288b6507708c221a61209267b2423481896a6d89b34154adb20d Section: science Priority: optional Homepage: http://search.cpan.org/~whizdog/GDGraph-histogram/ Description: Histogram plotting module for Perl5 GD::Graph::histogram extends the GD::Graph module to create histograms. The module allow creation of count or percentage histograms. Original-Maintainer: Snehanshu Shah Package: libinline-cpp-perl Version: 0.74-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: perl (>= 5.0), libinline-perl (>= 0.53), libparse-recdescent-perl Recommends: g++ Filename: ./libinline-cpp-perl_0.74-0lbi_amd64.deb Size: 45124 MD5sum: 7ff851048a1ee8400f14b458951b197c SHA1: ebb6b9197160e08a38b3d1474d423774469b0e36 SHA256: e4200c8c3198d804319fe0c2b7ea7784b807ba41d63a06e4aee6c2bda6499271 Section: science Priority: optional Homepage: http://github.com/daoswald/Inline-CPP Description: Write Perl subroutines and classes in C++ Inline::CPP lets you write Perl subroutines and classes in C++. You don't have to learn XS or SWIG, you can just put code right "inline" in your source. Original-Maintainer: David J. Oswald Package: libperl-unsafe-signals-perl Version: 0.03-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: perl Filename: ./libperl-unsafe-signals-perl_0.03-0lbi_amd64.deb Size: 27720 MD5sum: 7993716683f0429f28fe4b72b259333d SHA1: 8cacd0a4934ac2578ab2c040dd4cad37e9ce8ed6 SHA256: c9447f9a49fdc2edcf2a9e24c132bd9a7b4fb180056181d7c71516907f1ea4b9 Section: science Priority: optional Homepage: https://github.com/rgs/Perl-Unsafe-Signals Description: Allow unsafe handling of signals in selected blocks Allows to enable unsafe signal delivery just for a short period of time. Original-Maintainer: Rafael Garcia-Suarez Package: libpirobject-perl Version: 1.19-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: perl Filename: ./libpirobject-perl_1.19-0lbi_all.deb Size: 41096 MD5sum: 908a81650ff190ffa52bef196ec53d2d SHA1: ceabf20148cf288530288f6bd435571e6188bb11 SHA256: 7c5d7a27caddb16358d93e61f091599dec29b2dba3a1e1a291caf813ae1853f0 Section: science Priority: optional Homepage: https://github.com/prioux/PirObject Description: A Perl data model libray This perl library provides a simple way to model data objects. . There is little need for such a library in the modern programming world, it is here mostly as service to historical systems built using it. Original-Maintainer: Pierre Rioux Package: librdp-readseq-java Version: 0.1.20150512-0biolinux1 Architecture: all Maintainer: Tim Booth Installed-Size: 461 Depends: libcommons-cli-java, libcommons-io-java, libcommons-lang-java Filename: ./librdp-readseq-java_0.1.20150512-0biolinux1_all.deb Size: 424428 MD5sum: 6c33273ae3d86f76896d39ee4e721f5c SHA1: 2915b539fe7562a40ac54ff91fc35846905e9eb9 SHA256: 7ab9685f46f4fa85b181ccf2e40fe0cbe84d763cf64e6cf13d1460b8986d5f8b Section: java Priority: extra Description: RDP sequence reading and writing library Sequence reading library developed by the Ribosomal Database Project. Can handle genbank, embl, fasta, fastq, sff and sto files. Can read from files or streams, and can handle indexing files. . A basic rdp-readseq command line program is also included. . The ReadSeq project is a library used by other RDP tools Package: macs2 Version: 2.2.7.1-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3 (>= 3.6), python3-numpy (>= 1.13) Filename: ./macs2_2.2.7.1-1lbi_amd64.deb Size: 1215732 MD5sum: 6319ba2b488a7e4c2054a67f73fc5e99 SHA1: 6ac47dba42f15bb0479d87abfe4df26be3c7550e SHA256: 874a53c09f4c94360bf04dc63ac4e778717bec5ee75c7433d99cc08f57813427 Section: science Priority: optional Homepage: http://github.com/taoliu/MACS/ Description: Model-based Analysis for ChIP-Seq data With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we presented the Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity. Moreover, as a general peak-caller, MACS can also be applied to any "DNA enrichment assays" if the question to be asked is simply: 'where we can find significant reads coverage than the random background'. Original-Maintainer: Tao Liu Package: mash Version: 2.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./mash_2.0-0lbi_amd64.deb Size: 476238 MD5sum: d142472a1893221e6b534fda2fe058a8 SHA1: 163d142b5b1a841a24970482d28bd482eef3551c SHA256: a8ed59e41cfe7dab805fb42e2bf28e78fa101b59b8c695db9d0dd82a03bad827 Section: science Priority: optional Homepage: http://mash.readthedocs.org Description: Genome and metagenome distance estimation Fast genome and metagenome distance estimation using MinHash. Original-Maintainer: Adam M. Phillippy Package: masurca Version: 3.3.3-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: jellyfish, libboost-dev, libjellyfish-2.0-2, celera Filename: ./masurca_3.3.3-2lbi_amd64.deb Size: 61567732 MD5sum: b2b79d7960e5f1651037d4897fc17d84 SHA1: 590ce9dac64ea9ce97f3ab82e684719d498fb8a1 SHA256: 091ec1b88a4389698f48db49dcf3833b48fdb5540a52ee2c1c6490971c44d194 Section: science Priority: optional Homepage: https://github.com/alekseyzimin/masurca Description: Maryland Super Read Cabog Assembler The MaSuRCA assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly approaches. Since version 3.2.1 it supports hybrid assembly with short Illumina reads and long high error PacBio/MinION data. . MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads. Original-Maintainer: Aleksey Zimin , Guillaume Marçais Package: maxbin Version: 2.2.1-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bowtie2, fraggenescan, hmmer, idba, libwww-perl, r-cran-gplots Filename: ./maxbin_2.2.1-1lbi_amd64.deb Size: 2842004 MD5sum: 50f1379653a6a890eff59a1f62f538fa SHA1: e3b51461e0a686f6aba5eee80dbd771f68916064 SHA256: 35d11cb9794810d5959006452bfc0c176fcec076d89af68d3d4abf63215ac840 Section: science Priority: optional Homepage: http://downloads.jbei.org/data/MaxBin.html Description: MaxBin MaxBin is a software that is capable of clustering metagenomic contigs into different bins, each consists of contigs from one species. MaxBin uses the nucleotide composition information and contig abundance information to do achieve binning through an Expectation-Maximization algorithm. Original-Maintainer: Yu-Wei Wu Package: mdust Version: 1:0.1+20020708-2biolinux1.1 Architecture: amd64 Maintainer: Tim Booth Installed-Size: 77 Depends: libc6 (>= 2.14) Filename: ./mdust_1:0.1+20020708-2biolinux1.1_amd64.deb Size: 13828 MD5sum: 90a4d1d97aba5c2ac7752a3ab5427c5b SHA1: 1b385893be8303f20b672607b88e4aa03fb6a923 SHA256: 4752c57e0615a42bf4c69e724c4314583b8f944c8657662e8e3540d0a640c0f9 Section: science Priority: extra Description: repetitive sequence masker DUST is a fast C command-line utility that replicates the effect of BLAST's DUST filter. This package includes both mdust and the older dust. Package: medusa-scaffolder Version: 1.6-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: default-jre (>= 1.6), mummer, python-biopython (>= 1.61) Filename: ./medusa-scaffolder_1.6-1lbi_all.deb Size: 512272 MD5sum: 5fa2ff34006a6515206dc8d509dfa885 SHA1: 979355f21bbca0429ccb61341f5f4ea167a14af2 SHA256: f28d77aee59656d40640c908ae564d4781411c798986db2d920907f1e8de2216 Section: science Priority: optional Homepage: https://github.com/combogenomics/medusa Description: Genome scaffolder that uses multiple references Medusa is a draft genome scaffolder that uses multiple reference genomes in a graph-based approach. A web interface is available at http://combo.dbe.unifi.it/medusa Original-Maintainer: Marco Galardini Package: megahit Version: 1.1.4-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libopenmpi-dev, python2 (>= 2.7), zlib1g Suggests: nvidia-cuda-toolkit Filename: ./megahit_1.1.4-1lbi_amd64.deb Size: 6064732 MD5sum: 7aa4a8ea3427833cba57ec8365f580b1 SHA1: 0a02967ff38ead3c386768710cf81a52ed500fde SHA256: db85b8a294d7d1a04d29d33906c340e84d120099a652b52716d0003e4e654764 Section: science Priority: optional Homepage: https://github.com/voutcn/megahit Description: Large metagenomics assembly via succinct de Bruijn graph MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct *de Bruijn* graph (SdBG) to achieve low memory assembly. . MEGAHIT can **optionally** utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. Original-Maintainer: Dinghua Li Package: meme Version: 1:4.10.0.1-2lbi Architecture: amd64 Maintainer: Debian Med Packaging Team Depends: python2 (>= 2.7), python2 (<< 2.8), python2:any (>= 2.7.1-0ubuntu2), libc6 (>= 2.14), libxml2 (>= 2.7.4), libxslt1.1 (>= 1.1.25), csh, readseq, mdust Filename: ./meme_1:4.10.0.1-2lbi_amd64.deb Size: 1600812 MD5sum: 4ba1e90aee9cda03a56af21138a3fd3c SHA1: 889ed7c065d7293ca440331389985167afe1ac28 SHA256: 52524a18e21e0bdda4378dac75243fe0fdca379ffd5aec7c57981b8f05bab2e8 Section: non-free/science Priority: optional Homepage: http://meme.nbcr.net/meme/ Description: search for common motifs in DNA or protein sequences MEME (Multiple EM for Motif Elicitation) is a tool for discovering motifs in a group of related DNA or protein sequences. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns with variable-length gaps are split by MEME into two or more separate motifs. . MEME takes as input a group of DNA or protein sequences (the training set) and outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif. Package: metabat Version: 2.11.3-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libbam-dev, libboost-dev (>= 1.55.0), libncurses5-dev, python2 (>= 2.7), samtools, zlib1g-dev (>= 1.2.4) Filename: ./metabat_2.11.3-1lbi_amd64.deb Size: 9909604 MD5sum: 9917ed01ddb0aaf3dff89cdc8df2d708 SHA1: 60004aab56d7763df459ef3802d9d9fe03ad30d9 SHA256: 48a8b50c2d265ec706b3b3507833952f5f5a5bf1ce907934aebb197a67dfcefc Section: science Priority: optional Homepage: https://bitbucket.org/berkeleylab/metabat Description: MetaBAT reconstructs single genomes from microbial communities Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Here we developed an automated metagenome binning software, called MetaBAT, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. Tested on both synthetic and real metagenome datasets, MetaBAT outperforms alternative methods in both accuracy and computational efficiency. Original-Maintainer: Dongwan Kang , Rob Egan Package: metaeuk Version: 7-bba0d80-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./metaeuk_7-bba0d80-0lbi_amd64.deb Size: 51847284 MD5sum: 947f3436118101f71218b06d8c4be181 SHA1: e361f3b6fa6320440377b29e2757ab5a7cb6a65c SHA256: 2bd73fa294b478a6e63a5d1a323f6bde94d752eaa3f30110afa20bd3f8e435cb Section: science Priority: optional Homepage: https://github.com/soedinglab/metaeuk Description: Gene discovery and annotation for large-scale eukaryotic metagenomics MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to recover optimal exons sets. It reduces redundancies in multiple discoveries of the same gene and resolves conflicting gene predictions on the same strand. Original-Maintainer: Eli Levy Karin Package: metaphlan2 Version: 2.7.7-3lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2.7, python2 (>= 2.7), python2 (<< 2.8), python-numpy, python-biom-format, ncbi-blast+ (>= 2.2.25), bowtie2 (>= 2.0), python-matplotlib, python-scipy, python-pandas Replaces: metaphlan Filename: ./metaphlan2_2.7.7-3lbi_all.deb Size: 165232 MD5sum: bdc9d4569d8194a0a7a1eb6485b24b60 SHA1: dda63b2c19549f5ccc1a44eeff8bffe5702e8902 SHA256: 6ba9dbb0502275d93465db0b7d8179f93080d129ed768be02f3ea5bac4b314b8 Section: science Priority: optional Homepage: http://segatalab.cibio.unitn.it/tools/metaphlan2 Description: An enhanced metagenomic taxonomic profiling tool MetaPhlAn2 is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. . MetaPhlAn2 is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species. Original-Maintainer: Nicola Segata Package: metassembler Version: 1.5-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bowtie2, libstatistics-descriptive-perl, mummer, samtools, python2, python-argparse Filename: ./metassembler_1.5-2lbi_amd64.deb Size: 1110296 MD5sum: 3f8c6cfa7a9285fd6b71b74c523908e5 SHA1: fde5df30200cddeb5beba556afad18bff26146ad SHA256: cf0b0a3b7765452d4cd7d8d57af3e75c47a09145fa0b8d7472f3b324b726c6e9 Section: science Priority: optional Homepage: https://sourceforge.net/projects/metassembler/ Description: Combines multiple whole genome de novo assemblies Typically de novo genome sequencing projects generate multiple assemblies of the same sample using different software and/or different parameters of the same software. Instead of discarding the extra assemblies, Metassembler merges them to the top assembly using mate-pair information and whole-genome alignments, in order to generate a single superior assembly. The final assembly will combine the best locally superior assemblies throughout the genome. Original-Maintainer: Alejandro Hernandez Wences Package: metavelvet Version: 1.2.02-0biolinux1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 454 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.2.0.2), velvet Filename: ./metavelvet_1.2.02-0biolinux1_amd64.deb Size: 144332 MD5sum: b2478d2d9d00a40d98b83c53ae3e998b SHA1: ba289a7f899b3ff420ce9c3067ffdb58bfc08310 SHA256: c7708b0c84e439057234211791bcb4a3c8adc08a981430bdae62e418b4a093a7 Section: science Priority: optional Homepage: http://metavelvet.dna.bio.keio.ac.jp/ Description: extension of Velvet assembler to de novo metagenomic assembly An important step in metagenomics analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines use a single-genome assembler with carefully optimized parameters. A limitation of a single-genome assembler for de novo metagenome assembly is that sequences of highly abundant species are likely misidentified as repeats in a single genome, resulting in a number of small fragmented scaffolds. We extended a single-genome assembler for short reads, known as Velvet, to metagenomic assembly for mixed short reads of multiple species. . We modified and extended a single-genome and de Bruijn-graph based assembler, Velvet, for de novo metagenomic assembly. Our fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolated species genome. MetaVelvet has been proven to generate assemblies of longer N50 and higher quality than Velvet when applied to metagenomic sequences, and recognized as one of frequently-used metagenomic assemblers in this research community. Package: minimap Version: 2.11-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: k8, libc6 (>= 2.14), zlib1g (>= 1:1.1.4) Filename: ./minimap_2.11-0lbi_amd64.deb Size: 275020 MD5sum: 198b8f240587ac6ad2557534fb8da5fc SHA1: 96b3756bba17de9ebf1d95171f25f4ab24763bb9 SHA256: a9fc32314800598840a782d1b54d9c932830a3e51d8043fe27a11e372b70e689 Section: science Priority: optional Homepage: https://github.com/lh3/minimap2 Description: tool for approximate mapping of long biosequences such as DNA reads Minimap is an experimental tool to efficiently find multiple approximate mapping positions between two sets of long biological sequences, such as between DNA reads and reference genomes, between genomes and between long noisy reads. Minimap does not generate alignments as of now and because of this, it is usually tens of times faster than mainstream aligners. It does not replace mainstream aligners, but it can be useful when you want to quickly identify long approximate matches at moderate divergence among a huge collection of sequences. For this task, it is much faster than most existing tools. Original-Maintainer: Heng Li Package: miso Version: 0.5.4-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-matplotlib, python-numpy (>= 1.5.0), python-scipy (>= 0.9.0), python-pysam (>= 0.6.0) Recommends: bedtools, samtools Filename: ./miso_0.5.4-0lbi_amd64.deb Size: 1451310 MD5sum: bcd9f44543cd970b7fe11912e26ad29c SHA1: e03cd6e5a2c2fec051741c10075d3e56594e3364 SHA256: 91b70cfde26fd6b7391f04f01da5687e61085d863fb501f149bda742cf7f042a Section: science Priority: optional Homepage: http://genes.mit.edu/burgelab/miso/ Description: Mixture of Isoforms - isoform quantitation using RNA-Seq MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform. Original-Maintainer: Yarden Katz Package: mreps Version: 2.6-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./mreps_2.6-0lbi_amd64.deb Size: 48380 MD5sum: c1b0059bb0af8d25ac9f41f0d76d103d SHA1: 79f925708115e1e7d6f5afd466cf471ed5ba8d13 SHA256: 2eb80c99472e3309bcf3a3558253340ce71c91b96500d1791475533f17d98013 Section: science Priority: optional Homepage: http://mreps.univ-mlv.fr/ Description: Software for identifying tadem repeats in DNA sequences mreps is a flexible and efficient software for identifying serial repeats (usually called tandem repeats) in DNA sequences. Original-Maintainer: Gregory Kucherov Package: multiphate Version: 1.92-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: hmmer, ncbi-blast+ Filename: ./multiphate_1.92-1lbi_all.deb Size: 241824 MD5sum: 68c03eb62d08a1191eb3e4cd80d8720c SHA1: 39fb996c54d55964d4bb2dabefca03f82c48e3ed SHA256: 999ea5fe1a4aba9143e05b83fb4efcd220bac3e67731e8dbe2c879140900844b Section: science Priority: optional Homepage: https://github.com/carolzhou/multiPhATE2 Description: Annotation and comparison of phage genomes MultiPhATE is a command-line program that runs gene finding and the PhATE annotation code over user-specified phage genomes, then performs gene-by-gene comparisons among the genomes. Original-Maintainer: MultiPhATE developers Package: mytaxa Version: 0.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./mytaxa_0.0-0lbi_amd64.deb Size: 331912 MD5sum: d6478d41a9538cf7695bc84cb6f30244 SHA1: e38f547e539c703e1d1239612714dd7d7a7e5c9c SHA256: 888ab8ccbc9336f33ffd72565f3f87b309147c215a4b05bda68bb7070e5eb22c Section: science Priority: optional Homepage: http://enve-omics.ce.gatech.edu/mytaxa/index Description: Assign taxonomy to metagenomic fragments MyTaxa represents a new algorithm that extends the Average Amino Acid Identity (AAI) concept (Konstantinidis and Tiedje, PNAS 2005) to identify the taxonomic affiliation of a query genome sequence or a sequence of a contig assembled from a metagenome, including short sequences (e.g., 100-1,000nt long), and to classify sequences representing novel taxa at three levels (whenever possible), i.e., species, genus and phylum. . MyTaxa can assign a larger number of sequences and with higher accuracy compared to other tools available for the same purposes. This is largely attributed to the fact that MyTaxa considers all genes present in an unknown (query) sequence as classifiers and quantifies the classifying power of each gene using predetermined weights, which are derived from the analysis of orthologs of the gene from all available complete genomes. . MyTaxa also reports the statistical probability of the taxonomic assignment based on the Maximum Likelihood analysis. Original-Maintainer: Chengwei Luo , Konstantinos Konstantinidis Package: ncbi-acc-download Version: 0.2.6-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-biopython, python3-requests (>= 2.4.3) Filename: ./ncbi-acc-download_0.2.6-0lbi_all.deb Size: 12644 MD5sum: 6052db6753d23ee7dbaadefd7d3c1971 SHA1: 3253c56f092abb22137e919c83e93f1d5a14256b SHA256: 66c3ea400fef4cacb9d5c561c567a35a3830cab9011747aab375d1aaea210b26 Section: science Priority: optional Homepage: https://github.com/kblin/ncbi-acc-download Description: Download genome files from NCBI by accession A partner script to the popular ncbi-genome-download script, ncbi-acc-download allows you to download sequences from GenBank/RefSeq by accession through the NCBI [ENTREZ API](https://www.ncbi.nlm.nih.gov/books/NBK184582/). Original-Maintainer: Kai Blin Package: ncbi-blast+ Version: 2.17.0-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: ncbi-data, python3, perl:any Filename: ./ncbi-blast+_2.17.0-1lbi_amd64.deb Size: 236546016 MD5sum: 308e9b3f7f51e81e15aebd985271ee3b SHA1: 9249a5e78a1846d06be3799d0b1860b95ecb078a SHA256: 6201f7a366e288d2240749e60f7578b866a9dd4c2eabb34ba0bb18550383e704 Section: science Priority: optional Homepage: ftp://ftp.ncbi.nlm.nih.gov/blast Description: BLAST Command Line Applications The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Original-Maintainer: Christiam E. Camacho Package: ocfs2-tools Version: 1.8.6-2ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 3264 Pre-Depends: init-system-helpers (>= 1.54~) Depends: libaio1 (>= 0.3.93), libc6 (>= 2.14), libcmap4 (>= 1.99.9), libcom-err2 (>= 1.43.9), libdlm3 (>= 3.0.2), libglib2.0-0 (>= 2.24.0), libreadline8 (>= 6.0), libuuid1 (>= 2.16), debconf (>= 0.5) | debconf-2.0, psmisc, lsb-base (>= 3.0-6) Filename: ./third-party/ocfs2-tools_1.8.6-2ubuntu1_amd64.deb Size: 564220 MD5sum: 4fa4930310eb5494b84bb54c6b4c0a0a SHA1: b703fe89dfb8fa77cebce3515492d052f3d62956 SHA256: cb557d2a6ed7ee09befe285fb53e4291d2e7757ff6a9c49d75c5f3dfcf9c17c0 Section: admin Priority: optional Homepage: https://ocfs2.wiki.kernel.org/ Description: tools for managing OCFS2 cluster filesystems OCFS2 is a general purpose cluster filesystem. Unlike the initial release of OCFS, which supported only Oracle database workloads, OCFS2 provides full support as a general purpose filesystem. OCFS2 is a complete rewrite of the previous version, designed to work as a seamless addition to the Linux kernel. . This package installs the tools to manage the OCFS2 filesystem, including mkfs, tunefs, fsck, debugfs, and the utilities to control the O2CB clustering stack. Original-Maintainer: Debian HA Maintainers Package: octave-autopkgtest Source: octave-pkg-dev Version: 2.0.1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 20 Depends: gnuplot-nox Breaks: octave-pkg-dev (<= 1.5.0) Replaces: octave-pkg-dev (<= 1.5.0) Filename: ./third-party/octave-autopkgtest_2.0.1_all.deb Size: 4724 MD5sum: 4f20c234a928c5be85db44b8b897a23e SHA1: 01ce8e91c8ec06fca69603c975856606d05c278d SHA256: aa6631356b329109d769abbfade1b332499d10ba578e688446326c73a7ef3a3b Section: devel Priority: optional Description: script for automatic test of Octave add-on packages This package contains the check-pkg script (originally in the octave-pkg-dev package) that runs the unit tests contained in all *.m and *.cc files available in the source tree from which it is launched. It is intended to be used by the support for Octave-Forge add-on packages implemented in autodep8. . (Repackaged on Thu, 05 May 2022 18:08:42 -0300 by dpkg-repack.) Package: octave-pkg-dev Version: 2.0.1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 44 Depends: liboctave-dev (>= 4.0.0~rc3), octave-autopkgtest, debhelper (>= 11), cdbs, libmime-tools-perl, perl:any Filename: ./third-party/octave-pkg-dev_2.0.1_all.deb Size: 10232 MD5sum: fbd0fdc73a24d3ab55fb9ad921829dbf SHA1: 693022fec70e4cced785cd1ae284ea136012c087 SHA256: c502a3bb90d36e02dad30f4bfecdc15d9a57f6e7265db7c771a9537bf751e57d Section: devel Priority: optional Description: infrastructure to build Octave packages Since version 3.0 of Octave (a numerical computation software), add-ons can be installed through the pkg.m system. This package provides the infrastructure for packaging such add-ons for Debian. It contains a Makefile scrap for inclusion in debian/rules, as well as the necessary code for generating the appropriate maintainer scripts as well as the replacing the substitution variables in debian/control. . This package is intended to be used by the Debian Octave Group and should be of little interest to general users. . (Repackaged on Mon, 02 May 2022 16:18:14 -0300 by dpkg-repack.) Package: ontologizer Version: 2.1-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: graphviz Filename: ./ontologizer_2.1-0lbi_all.deb Size: 653480 MD5sum: fb2d0b8dff2db57b9b32bd15f9936cf1 SHA1: 41f31481ddbe770bd794c6bec6bf245cd506e9dd SHA256: 840dbed01db6914cf52eb18e9ed5ba0b3b4236cd3dcdf48bfa53f873dfbf4074 Section: science Priority: optional Homepage: http://ontologizer.de/ Description: Analyze and Visualize Biological Data Using Gene Ontology Ontologizer is a tool for the statistical analysis and visualization of high-throughput biological data using Gene Ontology. Original-Maintainer: Sebastian Bauer Package: parsnp Version: 1.5.2-2lb Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: fasttree, libmuscle1 (>= 3.7+4565), libgomp1 (>= 6), mummer, phipack, python3:any, python3-numpy, raxml Recommends: python3-dendropy Filename: ./parsnp_1.5.2-2lb_amd64.deb Size: 2987052 MD5sum: bd81925e63750454a02e45dd283190a2 SHA1: 59deb97de95b358473344c1914d11f498105f3a9 SHA256: 93e5e9099bd2e91f1a7ecaf99044c16166b7e8045df795956441ab972135d334 Section: science Priority: optional Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html Description: rapid core genome multi-alignment Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. Original-Maintainer: Todd J Treangen Package: pass-assembler Version: 0.3-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: perl Filename: ./pass-assembler_0.3-0lbi_all.deb Size: 71112 MD5sum: f0e453c55f79fbd83eef882d99e9903c SHA1: 06ab0ff08eb12dd7a8bcfec409704f9731d53eb3 SHA256: 7fb3a0cca24ef670d27cf327eb9d97c88b031363afbd902f32f4bbde5ebd0db1 Section: science Priority: optional Homepage: https://github.com/warrenlr/PASS Description: Proteome Assembler with Short Sequence peptide PASS is a proteomics application for de novo assembly of millions of very short (6 aa) to longer (100 aa) peptide sequences and beyond. It is derived from the popular genome assembler SSAKE, an easy-to-use, robust, reliable and tractable clustering algorithm for very short sequence reads, such as those generated by Illumina Ltd. Original-Maintainer: Rene L. Warren Package: pda Version: 1.0.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./pda_1.0.3-0lbi_amd64.deb Size: 1413688 MD5sum: c38b41c9e7d8ff305bffe9871109ea22 SHA1: aada39cb63782089bc057d771dc9d884ab48cd5f SHA256: bc75c33fe273d46fe423490e54079f60b3951a97130b0f7bf508d81dc6566d1f Section: science Priority: optional Homepage: http://www.cibiv.at/software/pda/ Description: Phylogenetic Diversity Analyzer A software tool for Biodiversity Analysis and Conservation Prioritization Problems. Original-Maintainer: Bui Quang Minh Package: phantomjs Version: 2.1.1+dfsg-2ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 1020 Depends: libc6 (>= 2.15), libgcc-s1 (>= 3.0), libqt5core5a (>= 5.12.2), libqt5gui5 (>= 5.0.2) | libqt5gui5-gles (>= 5.0.2), libqt5network5 (>= 5.3.0), libqt5printsupport5 (>= 5.2.0), libqt5webkit5 (>= 5.212.0~alpha3), libqt5widgets5 (>= 5.0.2), libstdc++6 (>= 5) Filename: ./third-party/phantomjs_2.1.1+dfsg-2ubuntu1_amd64.deb Size: 311832 MD5sum: 22a5e5098b625e16ae57a74b87ef1031 SHA1: 6bd56c8bd0dd957bc3f7ec9b42a813db5e37f8c5 SHA256: 1cf0d98fda7ca82d444f5f4a24a2244f19ac105b23924757e44a090854f8e18b Section: web Priority: extra Homepage: http://www.phantomjs.org/ Description: minimalistic headless WebKit-based browser with JavaScript API PhantomJS is a headless WebKit with JavaScript API. It has fast and native support for various web standards: DOM handling, CSS selector, JSON, Canvas, and SVG. . PhantomJS is an optimal solution for headless testing of web-based applications, site scraping, pages capture, SVG renderer, PDF converter and many other use cases. . (Repackaged on Mon, 02 May 2022 16:18:50 -0300 by dpkg-repack.) Package: phylophlan Version: 3.0.2-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: diamond-aligner (>= 0.9), fasttree (>= 2.1.8) | iqtree (>= 1.6.6) | raxml (>= 8.2.10), mafft (>= 7.310) | muscle (>= 3.8.1551), mash, ncbi-blast+ (>= 2.6.0), python3 (>= 3.7), python3-biopython (>= 1.73), python3-dendropy (>= 4.4.0), python3-matplotlib (>= 3.1.0), python3-numpy (>= 1.15.4), python3-pandas (>= 0.24.2), python3-seaborn (>= 0.9.0), trimal (>= 1.4.1) Filename: ./phylophlan_3.0.2-0lbi_all.deb Size: 75472 MD5sum: 5894b4ad5118977eccd498a4d8d11082 SHA1: fc0b06e62c69cac4376dbd598f240e4bb8529f67 SHA256: 3a073808939f6a84a5acf9dc57ad5137e604004cc0b4b09bec3902cd66e54072 Section: science Priority: optional Homepage: http://github.com/biobakery/phylophlan Description: Precise phylogenetic analysis of microbial isolates and genomes from metagenomes PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn can assign both genomes and metagenome-assembled genomes (MAGs) to species-level genome bins (SGBs). PhyloPhlAn can reconstruct strain-level phylogenies using clade-specific maximally informative phylogenetic markers, and can also scale to very-large phylogenies comprising >17,000 microbial species. Original-Maintainer: Francesco Asnicar Package: phylosift Version: 1.0.0-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: bioperl, bowtie2, fasttree, grinder, hmmer, infernal, last-align, libapp-cmd-perl, libbio-phylo-perl, libbiojava-java, pda, pplacer Filename: ./phylosift_1.0.0-2lbi_all.deb Size: 1909712 MD5sum: a0df23bb2cc155620af1ea82abee2f80 SHA1: d2fc6e6ce895fb917c5d600965968afe23ded1b2 SHA256: 9f8aeaeb7b5435fac6178d233c57031fb904813ae1408eaecaf92dfc4e5a5561 Section: science Priority: optional Homepage: https://github.com/gjospin/PhyloSift Description: Phylogenetic and taxonomic analysis for genomes and metagenomes PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes. . Using a reference database of protein and RNA sequences, PhyloSift can scan new sequences against that database for homologs and identify the phylogenetic relationship of the new sequence to the database sequences. During this procedure, high quality alignments of codon and amino acid sequence are generated. Original-Maintainer: Aaron Darling , Guillaume Jospin Package: plasmidfinder Version: 2.0.1-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: kma, ncbi-blast+, python3-pip Filename: ./plasmidfinder_2.0.1-2lbi_all.deb Size: 11768 MD5sum: 5b5552044887a8067e6640f55ac67ed1 SHA1: 80682d5d0441ccbc976f69d5c5e054924e31f11a SHA256: c1cb705576acc83f756ac84c1943925d413aa1c8ce87b0d11dfd4f15d42e1361 Section: science Priority: optional Homepage: https://cge.cbs.dtu.dk/services/PlasmidFinder/ Description: Finding plasmids PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria. Original-Maintainer: Henrik Hasman Package: platanus Version: 1.2.4-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libgcc1, libgomp1 Filename: ./platanus_1.2.4-0lbi_amd64.deb Size: 575254 MD5sum: 744f42bf0af5ecf42267c9724c5a68ec SHA1: 8917c0573264be7fae0af3a6b6711085d6b0bfad SHA256: 41138095ec9c4ce5c4c3aefa782b86355e5418aadcbe1cd8cdf740ddbb32e026 Section: science Priority: optional Homepage: http://platanus.bio.titech.ac.jp/ Description: PLATform for Assembling NUcleotide Sequences Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. Original-Maintainer: Rei Kajitani Package: pollux Version: 1.0.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./pollux_1.0.2-0lbi_amd64.deb Size: 33330 MD5sum: c854c4e37655e9a24541c13520eabf71 SHA1: 965fde0c9598240f677e07faa59ba0a2575cf60a SHA256: 156c5c1aff165d3d666d6acd0f12b0e91649ea1ee76b9f77f650195a83325e8f Section: science Priority: optional Homepage: https://github.com/emarinier/pollux Description: Platform independent error corrector Pollux is a platform independent error corrector which targets errors produced by second-generation sequencing technologies. Original-Maintainer: Brendan McConkey , Eric Marinier Package: pplacer Version: 1.1.alpha19-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 Recommends: python-biopython Filename: ./pplacer_1.1.alpha19-1lbi_amd64.deb Size: 5464500 MD5sum: 019221e9616e264b5d4f274eec6fd217 SHA1: b7570fcc64876a370acd0f90848992a4c1ab2f3a SHA256: cf4d5dec6b92dbf59d4d0691e129e00ed9bff92e5f495ca6e9ce9e0fdee545a0 Section: science Priority: optional Homepage: http://matsen.fhcrc.org/pplacer/ Description: Places sequences on a fixed reference phylogenetic tree Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. Original-Maintainer: Noah Hoffman Package: prinseq Version: 0.20.4-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: perl, libcairo-perl, libjson-perl Filename: ./prinseq_0.20.4-2lbi_all.deb Size: 419606 MD5sum: e144f3dbb1556a38698bfca6ccf6e668 SHA1: a8b2874b242f6190f99efe6b7c49006c5db2cb7f SHA256: d2b9bfd8f31135530359f1eb30d8615adba785dbadea80c9abf0197128323089 Section: science Priority: optional Homepage: http://prinseq.sourceforge.net/ Description: PReprocessing and INformation of SEQuence data PRINSEQ will help you to preprocess your genomic or metagenomic sequence data in FASTA or FASTQ format. Original-Maintainer: Robert Schmieder Package: prodigal Version: 1:2.6.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libc6 (>= 2.17) Filename: ./prodigal_1:2.6.3-0lbi_amd64.deb Size: 1077464 MD5sum: 2fbc11021e34dee7d0e1f796689304c7 SHA1: e275599713d03e2b2ff51e4c8d97090bbfca9b5c SHA256: eb0f34ec3deecd2328864c96e29f1fb9e41f791211cc57c2de46d42e2f162558 Section: science Priority: optional Homepage: http://prodigal.ornl.gov/ Description: Prokaryotic Dynamic Programming Genefinding Algorithm Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include: . Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less. . Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly). . Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%. . GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations. . Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown. . Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own. . Open Source: Prodigal source code is freely available under the General Public License. Original-Maintainer: Doug Hyatt Package: pullseq Version: 1.0.2-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libhts-dev, uthash-dev, zlib1g Filename: ./pullseq_1.0.2-1lbi_amd64.deb Size: 53748 MD5sum: 3640216a676cd50a925e76ac15907a58 SHA1: 9360587beda28bbeb6bafdd084b2065539aac224 SHA256: 2861e59064daef9200b42c4b22c54e22238361ecff717e245e826f27bfccdd86 Section: science Priority: optional Homepage: https://github.com/bcthomas/pullseq Description: Utility program for extracting sequences from a fasta/fastq file Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length. Fast, written in C, using kseq.h library. Original-Maintainer: Brian C. Thomas Package: pycharm Version: 3.1.3-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./pycharm_3.1.3-1lbi_amd64.deb Size: 94192472 MD5sum: 1d2dc2d90da5f738de0aa861b1063d7f SHA1: 84dcf785acc31c6bbaa6516b7919887bc638a87d SHA256: 05dce95f476a39c649686bdbf46386e6764c3d67df99fb35e32c9afe058e0f99 Section: science Priority: optional Homepage: https://www.jetbrains.com/pycharm/ Description: The intelligent Python IDE PyCharm is an Integrated Development Environment (IDE) used for programming in Python. It provides code analysis, graphical debugger, integrated unit tester, VCS/DVCS integration and supports web development with Django. Original-Maintainer: JetBrains Support Package: python-addict Version: 2.2.1-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Filename: ./python-addict_2.2.1-0lbi_all.deb Size: 6064 MD5sum: 39bf683415a5546ea395817306a1e1d9 SHA1: d0c99598449962eada8f376a000aaea6b846fd34 SHA256: 4dc72f81c34efe8de4df061a80efd6d4e18c8bfa7ca6f075a10b46c798993f4f Section: science Priority: optional Homepage: https://github.com/mewwts/addict Description: The Python Dict that's better than heroin Addict is a module that exposes a dictionary subclass that allows items to be set like attributes. Values are gettable and settable using both attribute and item syntax. Original-Maintainer: Mats Julian Olsen Package: python-backports-lzma Version: 0.0.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python Filename: ./python-backports-lzma_0.0.3-0lbi_amd64.deb Size: 38970 MD5sum: 238acedeaeb3f06d2d1a47c4392a67a5 SHA1: 8fca0535be1804a578ca6fb02d4b81c5f36bd1e7 SHA256: 72100031d070ec48b0cd779281b8723f80a0d5d4d041885575e5a9888d57f8d8 Section: science Priority: optional Homepage: https://github.com/peterjc/backports.lzma Description: Backport of python-lzma This is a backport of the 'lzma' module included in Python 3.3 or later by Nadeem Vawda and Per Oyvind Karlsen, which provides a Python wrapper for XZ Utils (aka LZMA Utils v2) by Igor Pavlov. Original-Maintainer: Peter Cock Package: python-backports.functools-lru-cache Version: 1.6.1-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7.5), python2 (<< 2.8) Filename: ./python-backports.functools-lru-cache_1.6.1-1lbi_amd64.deb Size: 8372 MD5sum: 5de894f20dae0e02feceea141896e9ce SHA1: 19b0148143098ac34b8ab017788000b62204eaf4 SHA256: 23b737bf864133fc13f3f78b6f916e2a4e3d38bbbdb92725dc11127cdf5ccb75 Section: python Priority: optional Homepage: https://github.com/jaraco/backports.functools_lru_cache Description: Backport of functools.lru_cache Backport of functools.lru_cache from Python 3.3 as published at ActiveState: Author: Raymond Hettinger Original-Maintainer: Jason R. Coombs Package: python-bcbio-gff Version: 0.5-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.4), python-support (>= 0.90.0) Filename: ./python-bcbio-gff_0.5-2lbi_all.deb Size: 13892 MD5sum: 1df14acc9e28d27c7084454661e3b3ad SHA1: 5a8f839dd405e7079f5ed77f6889b5f35c30297f SHA256: d53ded44f20f5f44be9a4575819f44f4900b819aaaa58d96257ce1e50954d393 Section: science Priority: optional Homepage: https://pypi.python.org/pypi/bcbio-gff/ Description: Read and write GFF with Biopython integration A python library to read and write Generic Feature Format (GFF). The goal is to integrate this code in gffutils and Biopython. Original-Maintainer: Brad Chapman Package: python-bioformats Version: 1.3.2-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-future, python-javabridge (>= 1.0) Filename: ./python-bioformats_1.3.2-1lbi_amd64.deb Size: 30021510 MD5sum: 42b3b99687f76d2e5b7510ad470ecc60 SHA1: 659f20ef24cc325308679c409df9f1a2fc44d7bf SHA256: ce6223318532ce3ab5ced1e16699b8ad55124db4b09a8d36caedd9bec4501d5f Section: science Priority: optional Homepage: http://github.com/CellProfiler/python-bioformats/ Description: Read and write life sciences file formats Python-bioformats is a Python wrapper for Bio-Formats, a standalone Java library for reading and writing life sciences image file formats. Bio-Formats is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. Python-bioformats uses the python-javabridge to start a Java virtual machine from Python and interact with it. Python-bioformats was developed for and is used by the cell image analysis software CellProfiler (cellprofiler.org). Original-Maintainer: Lee Kamentsky Package: python-biolib Version: 0.0.46-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-future (>= 0.15.2) Filename: ./python-biolib_0.0.46-0lbi_amd64.deb Size: 91612 MD5sum: 7e5f3289c881f2ae16d2445ec1507be7 SHA1: 0205d65cfa5fd711c479a6c234567a54b52fa665 SHA256: 065f1abb5ec9cfc535ca114d99f556bdc6908534777754bf785610814b7eafb7 Section: science Priority: optional Homepage: http://pypi.python.org/pypi/biolib/ Description: Package for common tasks in bioinformatic Biolib is a python package for common tasks in bioinformatic Original-Maintainer: Donovan Parks Package: python-biopython Version: 1.76-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: jython (>= 2.7), libc6 (>= 2.14), pypy (>= 7.1.1), python2 (>= 2.7), python2 (<< 2.8), python-matplotlib, python-numpy (>= 1:1.13.1) Recommends: ncbi-blast+, python-networkx, python-psycopg2, python-reportlab Suggests: clustalw, emboss, python-mysqldb Filename: ./python-biopython_1.76-2lbi_amd64.deb Size: 3760336 MD5sum: 41a1a3fa12c6f8ff9ab48a711cad6ed1 SHA1: 34f917ce88c11819a0ce557cc02c40449be20d8e SHA256: 47e898029133c901e531f7126ef0a7727688a3d91c5b29756c81a0910aded54f Section: python Priority: optional Homepage: http://biopython.org Description: Tools for computational molecular biology The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. Original-Maintainer: The Biopython Contributors Package: python-bnpy Version: 0.1.5-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython (>= 0.23.4), python2 (>= 2.7), python-joblib (>= 0.10.3), python-memory-profiler (>= 0.31), python-munkres (>= 1.0.7), python-numexpr (>= 2.6.1), python-numpy (>= 1.11.0), python-pandas (>= 0.18.1), python-psutil (>= 5.0.0), python-scikits-learn (>= 0.18.1), python-scipy (>= 0.17) Recommends: ipython (>= 2.4.1), python-matplotlib (>= 1.5.1) Filename: ./python-bnpy_0.1.5-2lbi_amd64.deb Size: 1673072 MD5sum: 21414111afee47c39823febdee6167d6 SHA1: 01b56bd2eb9ffc1d03f2f47d7bdabc8ccebdf25c SHA256: 59f930bb0bd554189eea14bb825c0ce67c37e9d701c7fbb232744d68490f9a9a Section: science Priority: optional Homepage: https://bnpy.readthedocs.io/en/latest/ Description: Bayesian nonparametric machine learning for python. This python module provides code for training popular clustering models on large datasets. We focus on Bayesian nonparametric models based on the Dirichlet process, but also provide parametric counterparts. . bnpy supports the latest online learning algorithms as well as standard offline methods. Our aim is to provide an inference platform that makes it easy for researchers and practitioners to compare models and algorithms. Original-Maintainer: Michael Hughes Package: python-brewer2mpl Version: 1.4.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python Recommends: python-matplotlib Filename: ./python-brewer2mpl_1.4.1-0lbi_amd64.deb Size: 25778 MD5sum: 733e2898f735d7539302e9ef8f4a7011 SHA1: a981e56f961ece43940beb1d5214127199afa520 SHA256: fea531969db8d2b6f9c1daf036bb1372476ecb4a3db8c8727e27d15d0663de79 Section: science Priority: optional Homepage: https://github.com/jiffyclub/brewer2mpl/wiki Description: Connect colorbrewer2.org color maps to Python Palettable (formerly brewer2mpl) is a library of color palettes for Python. It's written in pure Python with no dependencies, but it can supply color maps for matplotlib. You can use Palettable to customize matplotlib plots or supply colors for a web application. Original-Maintainer: Matt Davis Package: python-bz2file Version: 0.98-3lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 Filename: ./python-bz2file_0.98-3lbi_amd64.deb Size: 10592 MD5sum: abc4ec7ff32286a92bf57875849eb37b SHA1: 9862a6e0c7e0b306735d3a20a8788c28e1239530 SHA256: f7abe37de2e3a9881615abd9012256a4e264b89c44fbdd4ca9949fb371b17306 Section: science Priority: optional Homepage: https://github.com/nvawda/bz2file Description: Read and write bzip2-compressed files Bz2file is a Python library for reading and writing bzip2-compressed files. . It contains a drop-in replacement for the file interface in the standard library's ``bz2`` module, including features from the latest development version of CPython that are not available in older releases. . Bz2file is compatible with CPython 2.6, 2.7, and 3.0 through 3.4, as well as PyPy 2.0. Original-Maintainer: Nadeem Vawda Package: python-cobra Version: 0.4.0b4-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython (>= 0.20), python-brewer2mpl, python-cylp, python-dev, python-matplotlib, python-pandas, python-six Recommends: python-libsbml (>= 5.10), python-lxml, python-numpy (>= 1.6), python-scipy (>= 0.11.0) Filename: ./python-cobra_0.4.0b4-1lbi_amd64.deb Size: 948110 MD5sum: 6185bd29d90d9f0412df9853c6b1d6f5 SHA1: a94e3b72acb3072d2d252cdf1743e82383b43ddf SHA256: 3469932c20a7a7cfd7d44b7dae9842efa5a7d618e3e21511a44ec899577670b5 Section: science Priority: optional Homepage: https://opencobra.github.io/cobrapy Description: Constraints-based modeling of biological networks COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. COBRApy is a constraint-based modeling package that is designed to accomodate the biological complexity of the next generation of COBRA models and provides access to commonly used COBRA methods, such as flux balance analysis, flux variability analysis, and gene deletion analyses. Original-Maintainer: Daniel Robert Hyduke , Ali Ebrahim Package: python-colormath Version: 3.0.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python-networkx (>= 2.0), python-numpy Filename: ./python-colormath_3.0.0-0lbi_all.deb Size: 43944 MD5sum: 908307ff6770da12e5bfbd5764f322c4 SHA1: 2609c42f0126811f22710ce9663b6606c045a5c7 SHA256: 1b43b450eb9836e793eb4e494107d5a8072bc624037d7b26784f51ec8db74cbe Section: science Priority: optional Homepage: https://github.com/gtaylor/python-colormath Description: Color math and conversion library This module implements a large number of different color operations such as color space conversions, Delta E, and density to spectral. Original-Maintainer: Gregory Taylor Package: python-consensuscore Version: 1.0.0-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: dh-python, python2 (>= 2.7), python2 (<< 3), swig (>= 2.0.7), libboost-dev (>= 1.47.0) Recommends: quiver Filename: ./python-consensuscore_1.0.0-2lbi_amd64.deb Size: 4733980 MD5sum: eef291d89aff783a7429aecc2224c9e7 SHA1: 45a97f51b9f881041c362c924a7b733eeb8fbd20 SHA256: 0c5da273ca178e9c4f5eeb8040c27709d86859365009d7f2882c6d2e9bd67c6c Section: science Priority: optional Homepage: http://www.github.com/PacificBiosciences/ConsensusCore Description: Library for PacBio multiple sequence consensus ConsensusCore is a library of C++ algorithms for PacBio multiple sequence consensus that powers Quiver (Python). Original-Maintainer: Pacific Biosciences Package: python-cycler Version: 0.10.0-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7.5), python2 (<< 2.8), python-six Suggests: python-cycler-doc Filename: ./python-cycler_0.10.0-1lbi_amd64.deb Size: 10588 MD5sum: ae95e2c99401c3c6c455d6ac10b042f6 SHA1: 55e6852147a639bde491d6c807d2405896dd5336 SHA256: 5afc3958c229822dd8a1d205635ffcb37c5ec148a252247754d7a464db478cff Section: python Priority: optional Homepage: http://matplotlib.org/cycler/ Description: Composable style cycles When using matplotlib and plotting more than one line, it is common to want to be able to cycle over one or more artist styles; but the plotting logic can quickly become very involved. . To address this and allow easy cycling over arbitrary 'kwargs' the `Cycler` class, a composable kwarg iterator, was developed. Original-Maintainer: Thomas A Caswell Package: python-cylp Version: 0.7.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: coinor-cbc, coinor-clp, coinor-libcbc-dev, coinor-libcgl-dev, coinor-libclp-dev, python-numpy (>= 1.5.0), python-scipy (>= 0.10.0) Filename: ./python-cylp_0.7.2-0lbi_amd64.deb Size: 2328298 MD5sum: 0f81d8090f896276367aa4c6253b8b06 SHA1: 1cf7d8f6bdad8e9675093c905ad6f25155cb2e75 SHA256: 491fcff0baff5530383a5fc82f0170dd99652b8cb6d574390b541fec18a4026d Section: science Priority: optional Homepage: https://github.com/coin-or/CyLP Description: Interface to CLP, CBC, and CGL to solve LPs and MIPs CyLP is a Python interface to COIN-OR’s Linear and mixed-integer program solvers (CLP, CBC, and CGL). CyLP’s unique feature is that you can use it to alter the solution process of the solvers from within Python. For example, you may define cut generators, branch-and-bound strategies, and primal/dual Simplex pivot rules completely in Python. Original-Maintainer: Mehdi Towhidi , Dominique Orban Package: python-dateutil Version: 2.8.1-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7.5), python2 (<< 2.8), python-six (>= 1.5) Filename: ./python-dateutil_2.8.1-1lbi_all.deb Size: 225028 MD5sum: 795fd035de97479510687f8b7e2597f8 SHA1: dbba6427348fa50be8a491a92bbd3b9688ae6362 SHA256: 9319604226db0e7171e7959a2c853471c95e263ab12fde378f77bb0243722797 Section: python Priority: optional Homepage: https://dateutil.readthedocs.io Description: Extensions to the standard Python datetime module The dateutil module provides powerful extensions to the standard datetime module, available in Python. Author: Gustavo Niemeyer Original-Maintainer: Paul Ganssle Package: python-ete2 Version: 2.3.10-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-lxml, python-numpy, python-qt4 Filename: ./python-ete2_2.3.10-0lbi_amd64.deb Size: 769654 MD5sum: 19cfb71b55effd2c063fe24e3a5072c3 SHA1: c55cd30dc6f3ce7555b514a697605e2322910dc9 SHA256: d916ed01b087d04c72f5dc438c8455b64cfad61bd1671ea5b2d7ab5eb2b7a43c Section: science Priority: optional Homepage: http://etetoolkit.org Description: A Python Environment for (phylogenetic) Tree Exploration The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure could be used). . ETE is currently developed as a tool for researchers working in phylogenetics and genomics. If you use ETE for a published work, please cite: Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 2010, 11:24. Original-Maintainer: Jaime Huerta-Cepas Package: python-ete3 Version: 3.0.0b29-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-six Recommends: python-qt4 Filename: ./python-ete3_3.0.0b29-2lbi_amd64.deb Size: 3290448 MD5sum: 8d191f78f9235ba0e1d38712e5a735ac SHA1: 9cb59983c61ebe30a3f1cb8b60d131fbd49c3d82 SHA256: 2aa096c926277758d427fe8f4fe82f09b47770311804fe04baca05fa1b604bef Section: science Priority: optional Homepage: http://etetoolkit.org/ Description: A Python Environment for (phylogenetic) Tree Exploration The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported). Original-Maintainer: Jaime Huerta-Cepas Package: python-fastcluster Version: 1.1.22-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-numpy Filename: ./python-fastcluster_1.1.22-0lbi_amd64.deb Size: 264964 MD5sum: 2aec6fc89fcefc204639c40e748c8607 SHA1: c71ce41526639a077fc24f658e888a418f57a827 SHA256: 91c5cca2a3ac31241de1d5fa7096710476c7195f6547db5e6542c94aaba9e0de Section: science Priority: optional Homepage: http://danifold.net/fastcluster.html Description: Fast hierarchical clustering routines for R and Python This library provides Python functions for hierarchical clustering. It generates hierarchical clusters from distance matrices or from vector data. Original-Maintainer: Daniel Müllner Package: python-functools32 Version: 3.2.3-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python Filename: ./python-functools32_3.2.3-2lbi_amd64.deb Size: 21808 MD5sum: 6c64478ccb384aa79cf7acd6c5be77c3 SHA1: 012398ccb1d89d75a547b8d208c35e044d4e5eec SHA256: c8a4670e224c3cfd75598313b2bd02a21a6c4c9ac851754ad1323f5b296ac649 Section: science Priority: optional Homepage: https://github.com/MiCHiLU/python-functools32 Description: Backport of the functools module from Python 3.2.3 for use on 2.7 and PyPy This is a backport of the functools standard library module from Python 3.2.3 for use on Python 2.7 and PyPy. It includes new features `lru_cache` (Least-recently-used cache decorator). Original-Maintainer: Endoh Takanao Package: python-gensim Version: 0.12.3-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-numpy (>= 1.3), python-scipy (>= 0.7.0), python-six (>= 1.5.0) Filename: ./python-gensim_0.12.3-1lbi_amd64.deb Size: 2233280 MD5sum: 5a515b91a2e208a704d46386d6f6f1e6 SHA1: a26d8e7f7df744cb36b47857ced84f6e7cef4dcb SHA256: 4243c53c00c092d881383ae32ecf24f340ff6c46a820072225d0da9ef76dff5a Section: science Priority: optional Homepage: http://radimrehurek.com/gensim Description: Python framework for fast Vector Space Modelling Gensim is a Python library for *topic modelling*, *document indexing* and *similarity retrieval* with large corpora. Target audience is the *natural language processing* (NLP) and *information retrieval* (IR) community. Original-Maintainer: Radim Rehurek Package: python-gneiss Version: 0.4.5-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-biom-format, python3-ipython (>= 3.2.0), python3-matplotlib (>= 1.4.3), python3-numpy (>= 1.13.3), python3-pandas (>= 0.18.0), python3-scipy (>= 0.15.1), python3-skbio (>= 0.5.1), python3-seaborn, python3-statsmodels (>= 0.8.0) Filename: ./python3-gneiss_0.4.5-0lbi_all.deb Size: 32016 MD5sum: 4ad1c34f5958d4ab5ef7072c2257a409 SHA1: d0cefbd7971bd22a36b54dc0227a040b6706da96 SHA256: 9aa835fa0b48b698b63a3d3486bc0ff8bc7974bfd7196d1ff56603aa0b39423a Section: science Priority: optional Homepage: https://biocore.github.io/gneiss/ Description: Compositional data analysis tools and visualizations gneiss is a compositional data analysis and visualization toolbox designed for analyzing high dimensional proportions. See https://biocore.github.io/gneiss/ for API documentation. Original-Maintainer: gneiss development team Package: python-helperlibs Version: 0.1.5-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python, python-biopython (>= 1.62) Filename: ./python-helperlibs_0.1.5-0lbi_amd64.deb Size: 27730 MD5sum: 9ecd76097d4f0e626ea443f0af29920d SHA1: fba678ba0f1d4515e8b757f33c5a1b34aa6fb972 SHA256: bdc941f11966aa4c43d1bf2f5dfaa3ffe25590044b77d71e49e31a2b5283eca8 Section: science Priority: optional Homepage: https://github.com/kblin/bioinf-helperlibs/wiki Description: Bioinformatics-related helper functions This library is a collection of Bioinformatics-related helper functions that I have created in the course of writing bioinformatics tools. If I find that I want to reuse a bit of code in multiple projects, the code usually ends up in this helper library Original-Maintainer: Kai Blin Package: python-htseq Version: 0.6.1p1-4lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7), python2 (<< 2.8), python-numpy Filename: ./python-htseq_0.6.1p1-4lbi_amd64.deb Size: 495836 MD5sum: 0cb99a3560d8d5b61143569ff937a95b SHA1: 9b48bbd9a7f4deffafcef17c96566dfa822a8155 SHA256: 2643ae13b8f4d8700777b7ff201af0c37791b097904bf49eeb21614bef6c09bd Section: science Priority: optional Homepage: http://www-huber.embl.de/users/anders/HTSeq/ Description: High-throughput genome sequencing read analysis utilities HTSeq can be used to performing a number of common analysis tasks when working with high-throughput genome sequencing reads: . * Getting statistical summaries about the base-call quality scores to study the data quality. * Calculating a coverage vector and exporting it for visualization in a genome browser. * Reading in annotation data from a GFF file. * Assigning aligned reads from an RNA-Seq experiments to exons and genes. Original-Maintainer: Simon Anders Package: python-javabridge Version: 1.0.15-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython (>=0.18.0), python-numpy Filename: ./python-javabridge_1.0.15-0lbi_amd64.deb Size: 1507384 MD5sum: 3de01ca4a03806865217d49666e2ac58 SHA1: 2283fee4339615e5ee7d11b45785dcd0570c7000 SHA256: 1b6c6311aeb087698c2df0f344c1bf8481a44f541d01beafd945fa5d7bacba60 Section: science Priority: optional Homepage: http://github.com/CellProfiler/python-javabridge/ Description: Python wrapper for the Java Native Interface The javabridge Python package makes it easy to start a Java virtual machine (JVM) from Python and interact with it. Python code can interact with the JVM using a low-level API or a more convenient high-level API. . Python-javabridge was developed for and is used by the cell image analysis software CellProfiler (cellprofiler.org). Original-Maintainer: Lee Kamentsky Package: python-kiwisolver Version: 1.1.0-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7), python2 (<< 3) Filename: ./python-kiwisolver_1.1.0-1lbi_amd64.deb Size: 368180 MD5sum: 9cfacacaef4bd9b3b20b166246577fec SHA1: 69dd8e1403bf5fce2de36eb0bffcddd83b3c42b9 SHA256: 0701d625941dc8c9d45d5f7c7bc41696b7d5dad6f6b09d9d8abaeeb62fefb3a4 Section: science Priority: optional Homepage: https://github.com/nucleic/kiwi Description: A fast implementation of the Cassowary constraint solver Kiwi is an efficient C++ implementation of the Cassowary constraint solving algorithm. Kiwi is an implementation of the algorithm based on the seminal Cassowary paper. It is *not* a refactoring of the original C++ solver. Kiwi has been designed from the ground up to be lightweight and fast. Kiwi ranges from 10x to 500x faster than the original Cassowary solver with typical use cases gaining a 40x improvement. Memory savings are consistently > 5x. Original-Maintainer: The Nucleic Development Team Package: python-levenshtein Version: 0.12.2-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (<< 3) Filename: ./python-levenshtein_0.12.2-1lbi_amd64.deb Size: 86572 MD5sum: 24669f0d7b4baa805039522ea93988c7 SHA1: 21b786a38ebe5de6acc95f1aedc0719197553b0f SHA256: 00d13c72ac955491e6cd7fe5b45a4ca724af827ef6a3eb00a25e774ef1daa9de Section: science Priority: optional Homepage: https://github.com/ztane/python-Levenshtein Description: Python extension for computing string edit distances and similarities The Levenshtein Python C extension module contains functions for fast computation of * Levenshtein (edit) distance, and edit operations * string similarity * approximate median strings, and generally string averaging * string sequence and set similarity It supports both normal and Unicode strings. Original-Maintainer: Antti Haapala Package: python-libsbml Version: 5.11.4-4lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python Filename: ./python-libsbml_5.11.4-4lbi_amd64.deb Size: 12306428 MD5sum: 943638b3824a949a1d9b31c8f1cfa731 SHA1: 39b6b980b88124e4c0e14e2c812d5dcad1148138 SHA256: 9bd89d1a1265bd26eab193ada97266d39a2321fdab4a0d249e872949708713ff Section: science Priority: optional Homepage: http://sbml.org Description: LibSBML Python API LibSBML is a library for reading, writing and manipulating the Systems Biology Markup Language (SBML). It is written in ISO C and C++, and supports SBML Levels 1, 2 and 3. Original-Maintainer: SBML Team Package: python-louvain Version: 0.5-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-networkx Filename: ./python-louvain_0.5-1lbi_amd64.deb Size: 16364 MD5sum: 8a0c62f29953a31a548165a9c8092f28 SHA1: dc0a25384e6072e8b0edd634632b89fc29611afa SHA256: a4cd91a24e8ce92551640ed482671fa45d77f618ff32304ed8c1f7a24c4be303 Section: science Priority: optional Homepage: http://perso.crans.org/aynaud/communities/ Description: Louvain Community Detection Louvain algorithm for community detection Original-Maintainer: Thomas Aynaud Package: python-lzstring Version: 1.0.4-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python-future (>= 0.14.0) Filename: ./python-lzstring_1.0.4-0lbi_all.deb Size: 4844 MD5sum: 7de544a424a02a72706f0c72414d3646 SHA1: 6967af6ae02e83223a59f2af2f0939a7f2d25b44 SHA256: 33ea52f893b10de873515d1fe8215d35f4bfc57ebddc4a452a2376a87cf9be93 Section: science Priority: optional Homepage: https://github.com/gkovacs/lz-string-python Description: lz-string for python Based on the LZ-String javascript found here: http://pieroxy.net/blog/pages/lz-string/index.html Original-Maintainer: Geza Kovacs Package: python-mathstats Version: 0.2.6.5-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-scipy (>= 0.9), python-networkx (>= 1.4) Filename: ./python-mathstats_0.2.6.5-0lbi_amd64.deb Size: 30120 MD5sum: cd14e85c2e278207279a490b8140fe22 SHA1: a4ea64fc6899d5f34da47bf11e520b54345320e4 SHA256: 65e6b330e910cdb9c8ae397546a29a230c41791da9b78cca97fe3e513c37c97e Section: science Priority: optional Homepage: https://github.com/ksahlin/mathstats Description: Mathematical and statistical functions, distributions, tests Package mathstats contains mathematical and statistical functions, distributions, tests etc that is not included (at the moment) in scipy or numpy. Original-Maintainer: Kristoffer Sahlin Package: python-matplotlib Version: 2.2.5-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libfreetype6-dev (>= 2.3), libpng-dev (>= 1.2), python2 (>= 2.7), python2 (<< 3), python-backports.functools-lru-cache, python-cycler (>= 0.10.0), python-dateutil (>= 2.1), python-kiwisolver (>= 1.0.0), python-numpy, python-pyparsing, python-six, python-subprocess32, python-tz Suggests: ipython Filename: ./python-matplotlib_2.2.5-1lbi_amd64.deb Size: 7851384 MD5sum: 53d8a1a4254e4dd3e4b938d940be477f SHA1: 7fc382a78527e3b14d8ba11d2e22a9897d08cdeb SHA256: 38eb55da5fd1de08ad5ba36d448dab39e0041d2b4324413664f1bad610489ec9 Section: python Priority: optional Homepage: http://matplotlib.org/ Description: Python plotting package matplotlib strives to produce publication quality 2D graphics for interactive graphing, scientific publishing, user interface development and web application servers targeting multiple user interfaces and hardcopy output formats. There is a 'pylab' mode which emulates matlab graphics. Original-Maintainer: John D. Hunter and Michael Droettboom Package: python-matplotlib-venn Version: 0.11.6-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7.5), python2 (<< 2.8), python-matplotlib, python-numpy, python-scipy Filename: ./python-matplotlib-venn_0.11.6-1lbi_all.deb Size: 25232 MD5sum: e56cf33016e1e062544ec4109bde87bf SHA1: 0da66ea4af500a5036d2eb3e51339a89c91b2a8e SHA256: 98a8a1fec149e5ff6fc8c35ffaf7444cb74b94b82e10d019cd1576c0fccd45f8 Section: python Priority: optional Homepage: https://github.com/konstantint/matplotlib-venn Description: Routines for plotting area-weighted two- and three-circle venn diagrams Matplotlib is a pure Python plotting library designed to bring publication quality plotting to Python with a syntax familiar to Matlab users. All of the plotting commands in the pylab interface can be accessed either via a functional interface familiar to Matlab users or an object oriented interface familiar to Python users. Original-Maintainer: Konstantin Tretyakov Package: python-mpld3 Version: 0.3-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (<< 3) Filename: ./python-mpld3_0.3-1lbi_amd64.deb Size: 583936 MD5sum: b2f31e7fe70a07a7cd401211bfc7fb93 SHA1: 41c7e54780b603b3f8a635ab929e56c6872d36f1 SHA256: 00d9ce9ba69b91395fa67213f2df4f378d0691c4c4fc1bbae7ea99b737857e0d Section: science Priority: optional Homepage: http://mpld3.github.io/ Description: D3 Viewer for Matplotlib mpld3 provides a custom stand-alone javascript library built on D3, which parses JSON representations of plots. The mpld3 python module provides a set of routines which parses matplotlib plots (using the mplexporter framework) and outputs the JSON description readable by mpld3.js Original-Maintainer: Jake VanderPlas Package: python-mysqldb Version: 1.4.6-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: default-libmysqlclient-dev, libc6 (>= 2.4), python2 (>= 2.7), python2 (<< 2.8) Filename: ./python-mysqldb_1.4.6-1lbi_amd64.deb Size: 78448 MD5sum: c57c5a2ebc626507e3edd3cb63e2eeb4 SHA1: bdac39978c6557d72ee8884140994450c46c1f42 SHA256: 50759e0c9d11933a7bfd86329a499deb9099976f2b5c90cf8aed914cd204917a Section: python Priority: optional Homepage: https://github.com/PyMySQL/mysqlclient-python Description: Python interface to MySQL Mysqlclient is an interface to the popular MySQL database server for Python. Original-Maintainer: Inada Naoki Package: python-nacl Version: 1.4.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7), python-cffi (>= 1.14.0), python-six Filename: ./python-nacl_1.4.0-1lbi_all.deb Size: 732772 MD5sum: 96ca5ff8ecb014c1c8b49da70e87d939 SHA1: 6edbd6f3e83b5cf11062cba72151bcf61762e86e SHA256: c0d8c49bf98b2eb0cb32371832cfc0c3028925807a589f6b6dec5d8f999c20b9 Section: science Priority: optional Homepage: https://github.com/pyca/pynacl/ Description: Python binding to the Networking and Cryptography library (NaCl) PyNaCl is a Python binding to libsodium, which is a fork of the Networking and Cryptography library. These libraries have a stated goal of improving usability, security and speed. Original-Maintainer: The PyNaCl developers Package: python-networkx Version: 2.2-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-decorator, python2:any (<< 2.8), python2:any (>= 2.7.5-5~) Recommends: python-numpy, python-pkg-resources, python-yaml Suggests: python-matplotlib, python-pydotplus, python-scipy, python-pygraphviz | python-pydot Filename: ./python-networkx_2.2-1lbi_amd64.deb Size: 1641616 MD5sum: 78d10e82dda27dc76da8f95a3f471e1d SHA1: c5ffc504122c1684056bcbcb9809129fb13c9949 SHA256: 8dae1ff8c008ab7379888aad82d0a0bcd7c58946d550c85348c63ce72b7f524d Section: python Priority: optional Homepage: http://networkx.github.io/ Description: tool to create, manipulate and study complex networks NetworkX is a Python-based package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. . The structure of a graph or network is encoded in the edges (connections, links, ties, arcs, bonds) between nodes (vertices, sites, actors). If unqualified, by graph it's meant a simple undirected graph, i.e. no self-loops and no multiple edges are allowed. By a network it's usually meant a graph with weights (fields, properties) on nodes and/or edges. . The potential audience for NetworkX includes: mathematicians, physicists, biologists, computer scientists, social scientists. Original-Maintainer: NetworkX Developers Package: python-numpy Version: 1:1.16.6-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libopenblas-base (>= 0.2.15), python2 (>= 2.7), python2 (<< 2.8) Filename: ./python-numpy_1:1.16.6-2lbi_amd64.deb Size: 2851864 MD5sum: 123cff0282ba259b563af02952dde9ae SHA1: 16f18fd6d0a7256c5cfd28130510bf1409e4296b SHA256: 4851e129edae6f7d179115127bd9d060e9afd9e5ec646a4b33df272cec0a5ab8 Section: python Priority: optional Homepage: http://www.numpy.org/ Description: NumPy is the fundamental package for array computing with Python Numpy contains a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities. . Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. Author: Travis E. Oliphant et al. Original-Maintainer: NumPy Developers Package: python-pandas Source: pandas Version: 0.23.3-4lbi+1 Architecture: all Maintainer: NeuroDebian Maintainers Depends: neurodebian-popularity-contest, python2 (<< 2.8), python2 (>= 2.7), python-dateutil, python-numpy (>= 1:1.7~), python-tz, python2:any (>= 2.6.6-7~), python-pandas-lib (>= 0.23.3-1~nd18.04+1), python-pkg-resources, python-six Recommends: python-scipy, python-matplotlib, python-tables, python-numexpr, python-xlrd, python-statsmodels, python-openpyxl, python-xlwt, python-bs4, python-html5lib, python-lxml Suggests: python-pandas-doc Provides: python2.7-pandas Filename: ./python-pandas_0.23.3-4lbi+1_all.deb Size: 1743428 MD5sum: b39f836b06e017e2ada1ab88f6afcf20 SHA1: 83d8e65755253644043e00ea877b82c0af5a8a67 SHA256: 77f45f62f4709e09914a93945952fbe261cf1bb7dfc57887ef3dd6f4590a6070 Section: python Priority: optional Homepage: https://pandas.pydata.org/ Description: data structures for "relational" or "labeled" data pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with "relational" or "labeled" data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. pandas is well suited for many different kinds of data: . - Tabular data with heterogeneously-typed columns, as in an SQL table or Excel spreadsheet - Ordered and unordered (not necessarily fixed-frequency) time series data. - Arbitrary matrix data (homogeneously typed or heterogeneous) with row and column labels - Any other form of observational / statistical data sets. The data actually need not be labeled at all to be placed into a pandas data structure . This package contains the Python 2 version. Package: python-pandas-lib Source: pandas Version: 0.23.3-3lbi+1 Architecture: amd64 Maintainer: NeuroDebian Maintainers Depends: neurodebian-popularity-contest, libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2), python-numpy (>= 1:1.13.1), python2 (<< 2.8), python2 (>= 2.7) Provides: python2.7-pandas-lib Filename: ./python-pandas-lib_0.23.3-3lbi+1_amd64.deb Size: 3451160 MD5sum: 0b4de52568938a8dcf4aecd72088ebbf SHA1: 21c272d22555f1785b8ffe12c448042fd13cb2f3 SHA256: af4f236daddedce4cb5222a3038af52492c0038c531fbb256b2ba04e19bb8767 Section: python Priority: optional Homepage: https://pandas.pydata.org/ Description: low-level implementations and bindings for pandas This is an add-on package for python-pandas providing architecture-dependent extensions. . This package contains the Python 2 version. Python-Version: 2.7 Package: python-paramiko Version: 2.7.2-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7.5), python2 (<< 2.8), python-bcrypt (>= 3.1.3), python-cryptography (>= 2.5), python-nacl (>= 1.0.1), python-pyasn1 (>= 0.1.7) Suggests: python-gssapi (>= 1.4.1), python-invoke (>= 1.3) Filename: ./python-paramiko_2.7.2-2lbi_all.deb Size: 149396 MD5sum: 3ba8d5a931d00f6ab1a38f9f6f27382b SHA1: faae07041182fcdcff199f07ee52f9a213acaab4 SHA256: c5296331830f9febe549a750e42881440f1660236a10073d73dbee3ac50701e3 Section: python Priority: optional Homepage: https://github.com/paramiko/paramiko/ Description: SSH2 protocol library This is a library for making SSH2 connections (client or server). Emphasis is on using SSH2 as an alternative to SSL for making secure connections between Python scripts. All major ciphers and hash methods are supported. SFTP client and server mode are both supported too. Original-Maintainer: Jeff Forcier Package: python-pbcommand Version: 0.3.29-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./python-pbcommand_0.3.29-0lbi_amd64.deb Size: 140482 MD5sum: d844c2f5f66ad0d74332693b993f3230 SHA1: b0acc955c27a93f56959af91fb5b9fb9778e9f97 SHA256: 6ee96f177257904a0dfbc4b142fab1c1352d7ee78673a2ef5316326316f44c78 Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/pbcommand Description: Interface to PacBio pbsmrtpipe workflow engine PacBio library for common utils, models, and tools to interface with pbsmrtpipe workflow engine. Depedends: avro, ipython, python-autopep8, python-iso8601, python-jsonschema, python-pbcore, python-requests, python-xmlbuilder Original-Maintainer: Michael Kocher Package: python-pbcore Version: 1.2.7-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: cython, python-h5py (>= 2.0.1), python-numpy (>=1.7.1), python-pysam (>= 0.8.4) Filename: ./python-pbcore_1.2.7-0lbi_all.deb Size: 9072644 MD5sum: db73d7000b15ecdbc1eb5f3b03b632e0 SHA1: 19deca31f0ff0c6abe104e404120a2c8518cc425 SHA256: 17751903600cc6c5e40827a965cdf78cd48e3f46d3e2dd72f1b73eb6447601c2 Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/pbcore Description: Python library for reading and writing PacBio data files Python APIs for interacting with PacBio data files and writing bioinformatics applications. Original-Maintainer: Pacific Biosciences Package: python-pbh5tools Version: 2.3.0p4-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-h5py (>= 1.3.0), python-numpy (>= 1.6.0), python-pbcore (>= 0.8.0) Conflicts: pbh5tools Replaces: pbh5tools Filename: ./python-pbh5tools_2.3.0p4-2lbi_amd64.deb Size: 52996 MD5sum: 3993e78a076514853bfa5f366ef56cf7 SHA1: fadee3c7fbd3a565b6bb9dabc61275d9f4dc3bba SHA256: 45fa99f9f901e2ed2e8674b0fb5fbe87011daca6d199aedfec2ff52f1d500211 Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/pbh5tools Description: A swiss-army knife for interrogating PacBio HDF5 files Tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from "cmp.h5" and "bas.h5" files. Original-Maintainer: Pacific Biosciences Package: python-phylo-utils Version: 0.0.5-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython, python-numpy, python-dendropy Filename: ./python-phylo-utils_0.0.5-0lbi_amd64.deb Size: 321058 MD5sum: 8cda29314f3f73143c9b6c5111bf2bd1 SHA1: e2fd6089fcb1b84e5fd321f0e2df4981924a1202 SHA256: 6d0fd58fc6f4820ea50b08f772b0c7d43765ac6848b80b4bce8654797cb3ab55 Section: science Priority: optional Homepage: https://pypi.python.org/pypi/phylo_utils Description: Phylogenetics calculations in python Original-Maintainer: Kevin Gori Package: python-plotly Version: 1.12.2-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 Filename: ./python-plotly_1.12.2-2lbi_amd64.deb Size: 534932 MD5sum: c91452a0fa071e4702edfa513542d016 SHA1: 5d3118574f76e39b9ee85e6e34f2b5980fde902c SHA256: cfc393558d952d68581da0f1397fdfe84064b8d85bf370fa7b5dfe1703f4560f Section: science Priority: optional Homepage: https://plot.ly/python/ Description: Python plotting library for graphs Plotly is an online collaborative data analysis and graphing tool. The Python API allows you to access all of Plotly's functionality from Python. Plotly figures are shared, tracked, and edited all online and the data is always accessible from the graph. Original-Maintainer: Chris P Package: python-pyparsing Version: 2.4.7-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.6), python2 (<< 2.8) Filename: ./python-pyparsing_2.4.7-1lbi_all.deb Size: 108156 MD5sum: b00def099dea1ab2dbb763c448b2f279 SHA1: 1729a974fc96d1df91c3aacbbbb6497b0826c884 SHA256: 2dce656cb5f07830d1bc026fb89a2e7e00cfec5b878789d22fced41d5499b658 Section: python Priority: optional Homepage: https://github.com/pyparsing/pyparsing/ Description: Python parsing module The pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code. . (Since first writing this description of pyparsing in late 2003, this technique for developing parsers has become more widespread, under the name Parsing Expression Grammars - PEGs. See more information on PEGs at https://en.wikipedia.org/wiki/Parsing_expression_grammar) Original-Maintainer: Paul McGuire Package: python-pyqt5 Source: pyqt5 Version: 5.10.1+dfsg-3ubuntu2 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 13833 Depends: python2 (<< 2.8), python2 (>= 2.7~), python2:any (<< 2.8), python2:any (>= 2.7.5-5~), libc6 (>= 2.14), libqt5core5a (>= 5.9.2), libqt5dbus5 (>= 5.6.0~beta), libqt5designer5 (>= 5.9.1), libqt5gui5 (>= 5.9.0~beta3), libqt5help5 (>= 5.9.1), libqt5network5 (>= 5.9.0~beta), libqt5printsupport5 (>= 5.4.0), libqt5test5 (>= 5.6.0~beta), libqt5widgets5 (>= 5.9.0~beta), libqt5xml5 (>= 5.1.0), libstdc++6 (>= 5), qtbase-abi-5-9-5, sip-api-12.3 Suggests: python-pyqt5-dbg Filename: ./python-pyqt5_5.10.1+dfsg-3ubuntu2_amd64.deb Size: 2125588 MD5sum: a4bf05db1461bd1fa422dd3b50bb2704 SHA1: 19a856f487c10f7d5e863f868d5b361bb89f1282 SHA256: 1fda0a754fb1e4ce5f5c5f88f5bdaa60bd8e4c028866944e20affd6eaafffcc9 Section: python Priority: optional Homepage: http://www.riverbankcomputing.co.uk/software/pyqt/ Description: Python 2 bindings for Qt5 PyQt5 exposes the Qt5 API to Python 2. This package contains the following modules: * QtCore * QtDBus * QtDesigner * QtGui * QtHelp * QtNetwork * QtPrintSupport * QtTest * QtWidgets * QtXml Original-Maintainer: Debian Python Modules Team Package: python-pyquery Source: pyquery Version: 1.2.10-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python-lxml (>= 2.1), python-webob, python2 (>= 2.7.1-0ubuntu2), python2 (<< 2.8), python-cssselect (>> 0.7.9) Provides: python2.7-pyquery Filename: ./python-pyquery_1.2.10-0lbi_all.deb Size: 17440 MD5sum: 870378a901e1d54d954a7f6cda19e925 SHA1: f3a3d22a4d06823eaf2adaecaaa2c4133efd9341 SHA256: e0d7d43902078c2a0c4c53df73614dabd1a755cd0e3374f1e0228f33bda86414 Section: python Priority: extra Homepage: https://github.com/gawel/pyquery Description: A jQuery-like library for python pyquery allows you to make jQuery queries on XML documents. The API is as similar to jQuery as possible. pyquery uses lxml for fast XML and HTML manipulation. Original-Maintainer: Gael Pasgrimaud Package: python-pysam Version: 0.8.4-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.6), cython (>= 0.20) Filename: ./python-pysam_0.8.4-1lbi_amd64.deb Size: 5056492 MD5sum: fbd2bb6ad57f9dd911f1c9262ff3beaf SHA1: bb57f69bc26cb181b1a91f74d37ba23e4227ed4c SHA256: 93362df6ab86e343a07e42db72d60d02b2b3e0a00abc82963ad9c7d094f461ca Section: science Priority: optional Homepage: https://github.com/pysam-developers/pysam Description: Pysam Pysam is a python module for reading and manipulating files in the SAM/BAM format. The SAM/BAM format is a way to store efficiently large numbers of alignments (Li 2009), such as those routinely created by next-generation sequencing methods. Pysam is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. Original-Maintainer: Andreas Heger Package: python-pysvg Version: 0.2.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python Filename: ./python-pysvg_0.2.2-0lbi_amd64.deb Size: 45134 MD5sum: a79db16a4bd9be3b705cd5ef9e984ddd SHA1: 3c1782810216fe04f3239c66543d317d946d5101 SHA256: 581a0ad284f3d8d0e89f613ad37a921d5fe786fb413163e2cf825736de17d7d1 Section: science Priority: optional Homepage: http://codeboje.de/pysvg/ Description: Python SVG Library pySVG is a pure Python library to create SVG documents. Essentially it is a python wrapper around svg with the goal to allow people to "program svg". pySVG can be used to produce svg as an outcome of algorithms you implement (like koch curves, Lindenmayr systems etc.) Original-Maintainer: Kerim Mansour Package: python-ruffus Version: 2.5-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.4), python-support (>= 0.90.0) Filename: ./python-ruffus_2.5-1lbi_all.deb Size: 80548 MD5sum: a9892d36f90a6ab6c3c6a490c1bc0497 SHA1: 2a31c3884f07f64fdededa8c8cc40d9687c2e122 SHA256: 6f7892685f69f5c3d3372a5a2ec4a7a11caee9c56906199f9ce3b91c6a3b3d06 Section: science Priority: optional Homepage: http://www.ruffus.org.uk Description: Computation Pipeline library for python The Ruffus module is a lightweight way to add support for running computational pipelines. . Computational pipelines are often conceptually quite simple, especially if we breakdown the process into simple stages, or separate tasks. Each stage or task in a computational pipeline is represented by a python function. Each python function can be called in parallel to run multiple jobs. . Ruffus was originally designed for use in bioinformatics to analyse multiple genome data sets. Original-Maintainer: Leo Goodstadt Package: python-scipy Version: 1.0.0b1-3lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython (>= 0.23.4), python2 (>= 2.7), python2 (<< 2.8), python2-dev, python-numpy (>= 1.8.2) Filename: ./python-scipy_1.0.0b1-3lbi_amd64.deb Size: 16002812 MD5sum: 9bf826782b1afdf2f58a6cf463fb9ab9 SHA1: 0d22f3f7d4ad33aeabdda241ae4b205966b6c3b5 SHA256: 1f6522eada27cbfc9579559686f283ab14319e24a53255df57781566d07f2b8e Section: python2 Priority: optional Homepage: http://www.scipy.org/ Description: SciPy - Scientific Library for Python SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. The SciPy library depends on NumPy, which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. Together, they run on all popular operating systems, are quick to install, and are free of charge. NumPy and SciPy are easy to use, but powerful enough to be depended upon by some of the world's leading scientists and engineers. If you need to manipulate numbers on a computer and display or publish the results, give SciPy a try! Original-Maintainer: SciPy Developers Package: python-seaborn Version: 0.9.1-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (<< 2.8), python2 (>= 2.7.5), python-matplotlib (>= 1.5.3), python-numpy (>= 1.10.4), python-pandas (>= 0.17.1), python-scipy (>= 0.17.1) Filename: ./python-seaborn_0.9.1-1lbi_all.deb Size: 170828 MD5sum: 9280640a0583cddfbc406aa0ac5f2070 SHA1: e9b6b9a56af82ca092291f010c8cf039306f2237 SHA256: 588aadf66c9b27bdf2765c849586b8b90ecf336cc927a45e91b556670b448308 Section: science Priority: optional Homepage: https://seaborn.pydata.org Description: seaborn - statistical data visualization Seaborn is a library for making statistical graphics in Python. It is built on top of matplotlib and closely integrated with pandas data structures. . Seaborn aims to make visualization a central part of exploring and understanding data. Its dataset-oriented plotting functions operate on dataframes and arrays containing whole datasets and internally perform the necessary semantic mapping and statistical aggregation to produce informative plots. Original-Maintainer: Michael Waskom Package: python-six Version: 1.15.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7.5), python2 (<< 2.8) Filename: ./python-six_1.15.0-1lbi_all.deb Size: 13444 MD5sum: 6f2113541df5eb591ceee71a680f20cf SHA1: 350436bec9917bc0c05fd62507dec2139149cd58 SHA256: c5e03c555c76d3d2a9e91b650e35f849eeb2ffd310aa65f1cc7a0665ecee4c0c Section: python Priority: optional Homepage: https://github.com/benjaminp/six Description: Python 2 and 3 compatibility utilities Six is a Python 2 and 3 compatibility library. It provides utility functions for smoothing over the differences between the Python versions with the goal of writing Python code that is compatible on both Python versions. See the documentation for more information on what is provided. Original-Maintainer: Benjamin Peterson Package: python-spectra Version: 0.0.11-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python-colormath (>= 3.0.0) Filename: ./python-spectra_0.0.11-0lbi_all.deb Size: 20584 MD5sum: 5597fc6905d4c5d6816fd15cbc0f4f79 SHA1: 5f0dd6ccb47225eccee2c6c3a6f75917a9a9cf8f SHA256: e4bd199c194a4aa37800d76f78275c86477a382a8482eca056f8d1ff144419ae Section: science Priority: optional Homepage: http://github.com/jsvine/spectra Description: Easy color scales and color conversion for Python Spectra is a Python library that makes color math, color scales, and color-space conversion easy. Original-Maintainer: Jeremy Singer-Vine Package: python-straight-plugin Version: 1.4.0-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python Filename: ./python-straight-plugin_1.4.0-1lbi_amd64.deb Size: 7914 MD5sum: 2a213078de8112def00b7e4d4c0c63aa SHA1: f0fee191dd414de0868e6e309d1f29b322861823 SHA256: a21bd7c2675d0b1ec11573fafd1c2874f8f6c2c416c342f108e566573a17ca82 Section: science Priority: optional Homepage: https://github.com/ironfroggy/straight.plugin Description: A simple namespaced plugin facility Straight Plugin provides a type of plugin you can create from almost any existing Python modules, and an easy way for outside developers to add functionality and customization to your projects with their own plugins. Original-Maintainer: Calvin Spealman Package: python-subprocess32 Version: 3.5.4-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7), python2 (<< 2.8), libc6 (>= 2.9) Filename: ./python-subprocess32_3.5.4-1lbi_amd64.deb Size: 43436 MD5sum: cad657b2b2eed39790b59623d6cd5dce SHA1: 979017050e04a3fb0d75968d926b7d73a7c48bd1 SHA256: 2203a8b39fb35682d242a74ac33a06e61a1d0a5c941bc15675d4fa5f6ae8fc7b Section: python Priority: optional Homepage: https://github.com/google/python-subprocess32 Description: A backport of the subprocess module from Python 3 for use on 2.x This is a backport of the subprocess standard library module from Python 3.2 - 3.5 for use on Python 2. It includes bugfixes and some new features. On POSIX systems it is guaranteed to be reliable when used in threaded applications. It includes timeout support from Python 3.3 and the run() API from 3.5 but otherwise matches 3.2's API. Original-Maintainer: Gregory P. Smith Package: python-support Version: 1.0.15 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 155 Depends: python (>= 2.5), python-minimal, dpkg (>= 1.14.19) Conflicts: debhelper (<< 5.0.38) Filename: ./third-party/python-support_1.0.15_all.deb Size: 26672 MD5sum: 0d45e460d9fb2de50444bf59de240a6f SHA1: 60a7227c3a5a829f458a1e45a82672fb87702871 SHA256: 1b8498b47a08354026e7b43bb4dc42562c502e7c5def5d02b9f8837c043499f5 Section: python Priority: optional Description: automated rebuilding support for Python modules This package contains the 'update-python-modules' script, which takes care of byte-compilation of Python-only modules. . Private modules are automatically rebuilt upon major Python upgrades, avoiding the need for strong dependencies. . Public modules are automatically made available for all installed Python versions. Original-Maintainer: Josselin Mouette Package: python-toil Version: 3.19.0-2lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python-addict, python-dateutil, python-dill (>= 0.2.7.1), python-docker (>= 2.5.1), python-future, python-pathlib2 (>= 2.3.0), python-psutil (>= 3.0.1), python-requests (>= 2.18.4), python-requests (<< 3), python-six (>= 1.10.0), python-sphinx (>= 1.6.7), python-subprocess32 (<= 3.5.2) Filename: ./python-toil_3.19.0-2lbi_all.deb Size: 286400 MD5sum: 954c3af7359f30939ee01a6595cff8cd SHA1: 4daccc23334e5669b46515b76638688d3f118d94 SHA256: 8a2ef1aa6fa185b318511827a3265180323af266f1c212c83447ae47f047e04b Section: science Priority: optional Homepage: https://github.com/BD2KGenomics/toil Description: Pipeline management software for clusters Toil is a scalable and efficient pipeline management system, written entirely in Python, and designed around the principles of functional programming. Original-Maintainer: Benedict Paten Package: python-toolz Version: 0.8.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2.7 Filename: ./python-toolz_0.8.0-0lbi_amd64.deb Size: 79292 MD5sum: 1a006f41b41d98ef5c124a9e30b9d198 SHA1: e9d2be4a26a51dc38b1177926f251ebb7b83cd15 SHA256: 1506061a5fd0138d42da39915e830dabc279a25bf9d66b36eeb223af8f2b3439 Section: science Priority: optional Homepage: http://github.com/pytoolz/toolz/ Description: List processing tools and functional utilities A set of utility functions for iterators, functions, and dictionaries. See the PyToolz documentation at http://toolz.readthedocs.org Original-Maintainer: Matthew Rocklin Package: python-tree-distance Version: 1.0.6-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython Filename: ./python-tree-distance_1.0.6-0lbi_amd64.deb Size: 1382560 MD5sum: 0e8eb186df2ab80a472d62a70384bb73 SHA1: 359a23bea6a68d17dd8058538f44fb3478b71117 SHA256: c790a1d9153c1d39ce1f09aebdb1743960085ec59935f615ddfd48a1305c0610 Section: science Priority: optional Homepage: https://github.com/kgori/tree_distance.git Description: Wrapper for GTP tree distances in C++ Original-Maintainer: Kevin Gori Package: python-treecl Version: 0.1.29-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython (>= 0.19.0), ipython, python-biopython, python-concurrent.futures, python-dendropy (>= 4.0), python-fastcluster, python-matplotlib, python-nose, python-pandas, python-phylo-utils (>= 0.0.5), python-progressbar (>= 2.3), python-scipy, python-scikits-learn, python-skbio (>= 0.2.3), python-tree-distance (>=1.0.6), python-yaml Filename: ./python-treecl_0.1.29-1lbi_amd64.deb Size: 1081306 MD5sum: b79efe279c45c8ca156ee2a7e905e0c2 SHA1: 2781f98f8a90f9e41b06460aa34e682acfbacdd8 SHA256: acec3fec68e3a4645b22926aadb339e90f81ba30b7d6ceba46be0597d7a6d717 Section: science Priority: optional Homepage: https://github.com/kgori/treeCl Description: Phylogenetic Clustering Package treeCl is a python package for clustering gene families by phylogenetic similarity. It takes a collection of alignments, infers their phylogenetic trees, and clusters them based on a matrix of between-tree distances. Finally, it calculates a single representative tree for each cluster. Original-Maintainer: Kevin Gori Package: python-tz Version: 2020.4-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.4), python2:any (<< 2.8) Filename: ./python-tz_2020.4-1lbi_all.deb Size: 142988 MD5sum: 7850fe80caf0df6f9cade56b1d0c5ffd SHA1: 0d5dbee21fbd38e3adf5ccebd59c7005b05db897 SHA256: 3581f46e1fbbe67bbdad2e794ee959032cf26c132eb8c673725cf2bf77cdc8af Section: python Priority: optional Homepage: http://pythonhosted.org/pytz Description: World timezone definitions, modern and historical pytz brings the Olson tz database into Python. This library allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight saving time, which you can read more about in the Python Library Reference (datetime.tzinfo). Original-Maintainer: Stuart Bishop Package: python-unidecode Version: 1.1.1-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7), python2 (<< 2.8) Filename: ./python-unidecode_1.1.1-1lbi_all.deb Size: 117284 MD5sum: 9751f3921032615593cae293b59629ce SHA1: 446cc3cab1ff9e44b8d710ed32e37dbd5abe9cc8 SHA256: efebe3cbb443ecefa135b3074990d3bd1903ed7c5c336dfe27782b41914cf6f3 Section: python Priority: optional Homepage: https://pypi.python.org/pypi/Unidecode Description: ASCII transliterations of Unicode text It often happens that you have text data in Unicode, but you need to represent it in ASCII for display. One could represent non-roman Unicode characters as "???" or "\\15BA\\15A0\\1610", but neither is useful to the user reading the text. . Unidecode tries to represent it in ASCII characters (i.e., the universally displayable characters between 0x00 and 0x7F), where the compromises taken when mapping between two character sets are chosen to be near what a human with a US keyboard would choose. . This module generally produces better results than simply stripping accents from characters (which can be done in Python with built-in functions). It is based on hand-tuned character mappings that for example also contain ASCII approximations for symbols and non-Latin alphabets. . unidecode is a Python port of the Text::Unidecode Perl module. Original-Maintainer: Tomaz Solc Package: python-zmq Version: 19.0.2-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7), python2 (<< 2.8), libc6 (>= 2.14), libzmq5 (>= 4.1.2) Filename: ./python-zmq_19.0.2-1lbi_amd64.deb Size: 2508228 MD5sum: 93c0d7da191760e09f03accfa3cc1f3a SHA1: 2a9c3015118b1dc3e6227d5173d8ac8a854e948d SHA256: b86e593c08c10319b8f0c505e9265464273b3478e0fcef8f2f6633e5d0573817 Section: python Priority: optional Homepage: https://pyzmq.readthedocs.org Description: Python bindings for 0MQ library Python bindings for 0MQ. 0MQ is a small, fast, and free software library that gives you message-passing concurrency for applications in most common languages. . The 0MQ lightweight messaging kernel is a library which extends the standard socket interfaces with features traditionally provided by specialised messaging middleware products. 0MQ sockets provide an abstraction of asynchronous message queues, multiple messaging patterns, message filtering (subscriptions), seamless access to multiple transport protocols and more. Original-Maintainer: Brian E. Granger, Min Ragan-Kelley Package: python3-bcbio-gff Version: 0.6.6-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-six Filename: ./python3-bcbio-gff_0.6.6-1lbi_all.deb Size: 14292 MD5sum: 14a826117405b067cc1a8931fb1865da SHA1: 558abc843a1b9cd747b3e81487053db45d8e7299 SHA256: 2b3cfabcdf42aa893a3a448578d9bd1167ad5a83de920cf3d6e833f6052874d5 Section: science Priority: optional Homepage: https://github.com/chapmanb/bcbb/tree/master/gff Description: Generic Feature Format (GFF) for Biopython Read and write Generic Feature Format (GFF) with Biopython integration. Original-Maintainer: Brad Chapman Package: python3-bokeh Version: 1.3.4-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-dateutil (>= 2.1), python3-jinja2 (>= 2.7), python3-numpy (>= 1.7.1), python3-packaging (>= 16.8), python3-pil (>= 4.0), python3-six (>= 1.5.2), python3-tornado (>= 4.3), python3-yaml (>= 3.10) Filename: ./python3-bokeh_1.3.4-0lbi_all.deb Size: 5296208 MD5sum: 259ac4ba53678855d88b970bdecac484 SHA1: 235c0d73972abb7ac4847b01dbbdb2e389f11dd5 SHA256: 2263950bc72c18f8662f306211ed8f40ab0b7a5a44ddf2f7e3aea4c8a4aafd4e Section: science Priority: optional Homepage: http://github.com/bokeh/bokeh Description: Interactive plots and applications from Python Bokeh is an interactive visualization library for Python that enables beautiful and meaningful visual presentation of data in modern web browsers. With Bokeh, you can quickly and easily create interactive plots, dashboards, and data applications. . Bokeh provides an elegant and concise way to construct versatile graphics while delivering high-performance interactivity for large or streamed datasets. Original-Maintainer: Bokeh Team Package: python3-bx Version: 0.8.4-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3 (>= 3.3), python3-numpy, python3-six Filename: ./python3-bx_0.8.4-0lbi_amd64.deb Size: 2109012 MD5sum: 0d57fc87bc08634dd78f36182cedcd1a SHA1: 2733ddb79f5c1a61d44010c5b72f38e3dc4d65ad SHA256: 223a71902b09e5f9d4344db33de8ff5eb4061ea0d308d560de2873e8cdba4c34 Section: science Priority: optional Homepage: https://github.com/bxlab/bx-python Description: Tools for manipulating biological ata The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. Original-Maintainer: James Taylor Package: python3-cgecore Version: 1.5.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3 Filename: ./python3-cgecore_1.5.0-1lbi_all.deb Size: 30836 MD5sum: 6ed26d26cb0a8df5e6a71e528ef5bea6 SHA1: 9b0fc1dd434b302fef8455c4c520efc7fff85565 SHA256: ccfc46499ab31f95c596612aa09fad12d1b041e59fe34f4185bd1ae4c2256b7a Section: science Priority: optional Homepage: https://bitbucket.org/genomicepidemiology/cge_core_module Description: Center for Genomic Epidemiology Core Module This module contains classes and functions needed to run the service wrappers and pipeline scripts. Original-Maintainer: Center for Genomic Epidemiology Package: python3-deblur Version: 1.1.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-click (>= 6.0), python3-numpy (>= 1.7), python3-skbio (>= 0.5.0), python3-skbio (<< 0.6.0), python3-biom-format (>= 2.1.3), python3-biom-format (<< 2.2.0), python3-h5py (>= 2.2.0), python3-scipy (>= 0.15.1) Filename: ./python3-deblur_1.1.0-0lbi_all.deb Size: 1721168 MD5sum: 1e7aed1a86f06849e5b5316b319996f0 SHA1: e9f26de9d33e652037af152d1c185fbaf1ea7158 SHA256: fe4c163bff38a2e9d7d4fe9729a72cd3036f97c274fc3de7a17c7e8e942e29be Section: science Priority: optional Homepage: https://github.com/biocore/deblur Description: Greedy deconvolution algorithm Deblur is a greedy deconvolution algorithm for amplicon sequencing based on Illumina Miseq/Hiseq error profiles. Original-Maintainer: Deblur development team Package: python3-dnaio Version: 0.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3-xopen Filename: ./python3-dnaio_0.3-0lbi_amd64.deb Size: 299800 MD5sum: 7742c8d592442ef59f5cfa2549bb3104 SHA1: 4025cb234ea76673de06530c7716e178b9310cba SHA256: 2fdcc98fc997feaaa9cf046be699f9a1d3072d29f62d1b0034ac38dac9809745 Section: science Priority: optional Homepage: https://github.com/marcelm/dnaio/ Description: Read FASTA and FASTQ files efficiently dnaio is a Python 3 library for fast parsing of FASTQ and also FASTA files. The code was previously part of the Cutadapt tool and has been improved since it has been split out. Original-Maintainer: Marcel Martin Package: python3-edlib Version: 1.3.8.post1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3 Filename: ./python3-edlib_1.3.8.post1-0lbi_amd64.deb Size: 206304 MD5sum: c15b6e6857304d4818d58c2ba5f08a58 SHA1: 11360dfb6850b0a893fbd703c6eab6d211e287c5 SHA256: 64334683c5e3b209e9a4de5e3ede94db8ca7680907552373b333bd3d82dd5e97 Section: science Priority: optional Homepage: https://github.com/Martinsos/edlib Description: Sequence alignment using edit (Levenshtein) distance Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. Popular use cases: aligning DNA sequences, calculating word/text similarity. Original-Maintainer: Martin Sosic Package: python3-ete3 Version: 3.1.2-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-lxml, python3-numpy, python3-pyqt5, python3-six Filename: ./python3-ete3_3.1.2-0lbi_all.deb Size: 1687916 MD5sum: a509b79184186dba4b70168154aa5111 SHA1: d552b722eaac48599218fcc818eadea00e07fdbd SHA256: dd9a982ef7e7c046918a37e34f483137fdbb9693a32c2c5ce45b37bd9a6c49fd Section: science Priority: optional Homepage: http://etetoolkit.org Description: A Python Environment for phylogenetic Tree Exploration ETE (Environment for Tree Exploration) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees. Clustering trees or any other tree-like data structure are also supported. Original-Maintainer: Jaime Huerta-Cepas Package: python3-fair-esm Version: 2.0.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3 Filename: ./python3-fair-esm_2.0.0-1lbi_all.deb Size: 56220 MD5sum: 8ba007ce8a5aa2594bca9bba766d75f6 SHA1: e5b8d5e32c01f28a242b79d4f6a9e014599c25e3 SHA256: ec3a557ffea7e9c80c955dcc1ddca83fcb595410b0d9768cee80aff0a3b756b6 Section: science Priority: optional Homepage: https://pypi.org/project/fair-esm/ Description: Evolutionary Scale Modeling This repository contains code and pre-trained weights for **Transformer protein language models** from Facebook AI Research, including our state-of-the-art **ESM-2** and **ESMFold**, as well as **MSA Transformer**, **ESM-1v** for predicting variant effects and **ESM-IF1** for inverse folding. . Transformer protein language models were introduced in the preprint of the paper ["Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences" (Rives et al., 2019)](https://doi.org/10.1101/622803). Original-Maintainer: Maintainer Package: python3-filetype Version: 1.0.1-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./python3-filetype_1.0.1-1lbi_amd64.deb Size: 32654 MD5sum: e89b20b8f17845ad134130d9e2c7f7bc SHA1: dd434d2a1ff215204fc66d405b32d060b2cc56ca SHA256: de4d8658ae767657f935c1367a4eb46c26806754062271862294201325b8cdea Section: science Priority: optional Homepage: https://github.com/h2non/filetype.py Description: Infer file type and MIME type of any file/buffer Small and dependency free python package to infer file type and MIME type checking the magic numbers signature of a file or buffer. Original-Maintainer: Tomas Aparicio Package: python3-freetype-py Version: 2.1.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3, libfreetype6 Filename: ./python3-freetype-py_2.1.0-0lbi_all.deb Size: 119804 MD5sum: f068b417218fa3f43b666a46c5dda72b SHA1: 437d4ead28bb7b1705d95ea064028fcfc9b3423b SHA256: dd340d9a56f40a439cacad8a98569f1db5b552276589f1f8dd8dd5fb6649e575 Section: science Priority: optional Homepage: https://github.com/rougier/freetype-py Description: Freetype python bindings Freetype Python provides bindings for the FreeType library. Only the high-level API is bound. . Documentation available at http://freetype-py.readthedocs.org/en/latest/ Original-Maintainer: Nicolas P. Rougier Package: python3-gffutils Version: 0.10.1-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-argcomplete (>= 1.8.1), python3-argh (>= 0.26.2), python3-pyfaidx, python3-simplejson, python3-six Filename: ./python3-gffutils_0.10.1-0lbi_all.deb Size: 52432 MD5sum: ad68bc7c50d2a9cdc689b5f762c888ed SHA1: 5b31006dcce5c341d81b33e53d955afb7426419a SHA256: 0eeaeb2907f70c8ecc578ba7483b11ce893c21977140d00d81dbd4d1b27f1d85 Section: science Priority: optional Homepage: https://github.com/daler/gffutils Description: GFF and GTF file manipulation and interconversion gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. Files are loaded into a sqlite3 database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone. Original-Maintainer: Ryan Dale Package: python3-gnutls Version: 3.1.2-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3, libgnutls30 Filename: ./python3-gnutls_3.1.2-0lbi_all.deb Size: 35524 MD5sum: 8fb622a6a60eebf7eeaf2feb0d960114 SHA1: b936ffbc4de7c1580898b05cd34b3b36337ec1cd SHA256: 15a38a7753ee21fbd4fc70fc5f563017539f15444229061602ed44794b89e9c6 Section: science Priority: optional Homepage: https://github.com/AGProjects/python-gnutls Description: Python wrapper for the GnuTLS library This package provides a high level object oriented wrapper around libgnutls, as well as low level bindings to the GnuTLS types and functions via ctypes. The high level wrapper hides the details of accessing the GnuTLS library via ctypes behind a set of classes that encapsulate GnuTLS sessions, certificates and credentials and expose them to python applications using a simple API. . The package also includes a Twisted interface that has seamless intergration with Twisted, providing connectTLS and listenTLS methods on the Twisted reactor once imported (the methods are automatically attached to the reactor by simply importing the GnuTLS Twisted interface module). Original-Maintainer: Dan Pascu Package: python3-keras Source: keras Version: 2.2.4-1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 1502 Depends: python3-numpy, python3-scipy, python3-h5py, python3-theano, python3-keras-applications, python3-keras-preprocessing, python3-six (>= 1.9.0), python3-yaml, python3:any (>= 3.5~) Filename: ./third-party/python3-keras_2.2.4-1_all.deb Size: 202080 MD5sum: 35edeef5376a34e96a1a6fbc4f75dba1 SHA1: 9ddd8ff315552684c2ee6573dbbe5eb0e966740d SHA256: 907a87efd2d017625a34ccf0480efa340166a8c0fc8f34d1882c78ffcb6e7d60 Section: python Priority: optional Homepage: http://keras.io/ Description: deep learning framework running on Theano or TensorFlow Keras is a Python library for machine learning based on deep (multi- layered) artificial neural networks (DNN), which follows a minimalistic and modular design with a focus on fast experimentation. . Features of DNNs like neural layers, cost functions, optimizers, initialization schemes, activation functions and regularization schemes are available in Keras a standalone modules which can be plugged together as wanted to create sequence models or more complex architectures. Keras supports convolutions neural networks (CNN, used for image recognition resp. classification) and recurrent neural networks (RNN, suitable for sequence analysis like in natural language processing). . It runs as an abstraction layer on the top of Theano (math expression compiler) by default, which makes it possible to accelerate the computations by using (GP)GPU devices. Alternatively, Keras could run on Google's TensorFlow (not yet available in Debian). . (Repackaged on Mon, 02 May 2022 16:19:08 -0300 by dpkg-repack.) Package: python3-kiwisolver Version: 1.3.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3-setuptools Filename: ./python3-kiwisolver_1.3.1-0lbi_amd64.deb Size: 837728 MD5sum: c4e9da5258e01f6daf007ebece56fd9c SHA1: 73c516391a594073ffdd77df400438ecb28c2e21 SHA256: 517f230b07939d4dfbde648c1da72c8eb416f55249260bde9c173915ff97cc9f Section: science Priority: optional Homepage: https://github.com/nucleic/kiwi Description: A fast implementation of the Cassowary constraint solver Kiwi is an efficient C++ implementation of the Cassowary constraint solving algorithm. Kiwi is an implementation of the algorithm based on the seminal Cassowary paper. It is not a refactoring of the original C++ solver. Kiwi has been designed from the ground up to be lightweight and fast. Kiwi ranges from 10x to 500x faster than the original Cassowary solver with typical use cases gaining a 40x improvement. Memory savings are consistently > 5x. Original-Maintainer: The Nucleic Development Team Package: python3-mathstats Version: 0.2.6.5-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3-scipy (>= 0.9), python3-networkx (>= 1.4) Filename: ./python3-mathstats_0.2.6.5-0lbi_all.deb Size: 30060 MD5sum: 51df455b7099e964af62648c09d5e093 SHA1: 0ce19338603a5dfb5445b2a3440a1e3368f71598 SHA256: f5a9c11dfde98b437168b748f6980d93e91b072ac0ae5c092472f1655088c83f Section: science Priority: optional Homepage: https://github.com/ksahlin/mathstats Description: Mathematical and statistical functions, distributions, tests Package mathstats contains mathematical and statistical functions, distributions, tests etc that is not included (at the moment) in scipy or numpy. Original-Maintainer: Kristoffer Sahlin Package: python3-networkx Version: 2.4-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3, python3-decorator (>= 4.1.2), python3-lxml, python3-matplotlib, python3-numpy, python3-pandas, python3-scipy, python3-yaml, python3-pygraphviz | python3-pydot Filename: ./python3-networkx_2.4-1lbi_amd64.deb Size: 683004 MD5sum: 6a74221219333f221af1a316be889085 SHA1: 3320186392340a9ea61961f179bbbbd4f54a4062 SHA256: 1b59b69020e3a7e9b5be8ecfe5f9ab98a2dc9e616c84149879ff3234a0cda2e4 Section: python Priority: optional Homepage: http://networkx.github.io/ Description: Software for complex networks NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Original-Maintainer: NetworkX Developers Package: python3-py2bit Version: 0.2.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3 Filename: ./python3-py2bit_0.2.0-0lbi_amd64.deb Size: 30636 MD5sum: 36a38872b44202acde940aeb696a1dfa SHA1: 9aefac6273a02e5d5d34e1f15ee1a5918706f0b0 SHA256: 12892f82fea6f75a9da77fc3c414d3b1dad2e504947b9442aaff093d384a78b3 Section: science Priority: optional Homepage: https://github.com/dpryan79/py2bit Description: A package for accessing 2bit files using lib2bit A python extension, written in C, for quick access to 2bit files. The extension uses lib2bit for file access. Original-Maintainer: Devon P. Ryan Package: python3-pyahocorasick Version: 1.1.8-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3 Filename: ./python3-pyahocorasick_1.1.8-0lbi_amd64.deb Size: 49900 MD5sum: f0d2090fdffa214254729d52562e5217 SHA1: 2828a56441369cd05004a8c326bf7c0badd4e9f5 SHA256: 861e2166095b047a30517029be79326f235337e479b6953e426712f6229db267 Section: science Priority: optional Homepage: http://github.com/WojciechMula/pyahocorasick Description: Library for exact or approximate multi-pattern string search pyahocorasick is a fast and memory efficient library for exact or approximate multi-pattern string search meaning that you can find multiple key strings occurrences at once in some input text. The library provides an `ahocorasick` Python module that you can use as a plain dict-like Trie or convert a Trie to an automaton for efficient Aho-Corasick search. Original-Maintainer: Wojciech Muła Package: python3-pyani Version: 0.2.7-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3-biopython, python3-matplotlib, python3-pandas, python3-scipy, python3-seaborn Filename: ./python3-pyani_0.2.7-0lbi_amd64.deb Size: 79910 MD5sum: a6b3b8992f4ac967d2e84509225f4d82 SHA1: 2c1a4ee9572a33676d60617b98e2a83caf7a6ea1 SHA256: 127a8f3f80a99046c26597be2d015c2303b3390893bad7666a80c7832e0c86ed Section: science Priority: optional Homepage: http://widdowquinn.github.io/pyani/ Description: Calculation of genome-scale average nucleotide identity. pyani provides a package and script for calculation of genome-scale average nucleotide identity. Original-Maintainer: Leighton Pritchard Package: python3-pybigwig Version: 0.3.11-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3, python3-numpy Filename: ./python3-pybigwig_0.3.11-0lbi_amd64.deb Size: 120646 MD5sum: 2ad45632b87e18ca42be0d2cf96c92c3 SHA1: 691293f06bfc96b2ab33b3ec3fa31eb8aeca028f SHA256: 894163911e843854785c076fc6a3aea4713621f6c43c4c0f8064712bb5e5d772 Section: science Priority: optional Homepage: https://github.com/dpryan79/pyBigWig Description: A package for accessing bigWig files using libBigWig A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. This extension uses libBigWig for local and remote file access. Original-Maintainer: Devon P. Ryan Package: python3-pysam Version: 0.14-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython3 (>= 0.23.4) Filename: ./python3-pysam_0.14-1lbi_amd64.deb Size: 5882972 MD5sum: 10ca6c7e29e03a60b816090a78ca13f3 SHA1: 56f3c0574b285e949c96d43abd0fb21e5bbe8637 SHA256: 869198e774ddba742f0b53817e947587d2314a4e5825581b4b9552c19af8dd1b Section: science Priority: optional Homepage: https://github.com/pysam-developers/pysam Description: Pysam Pysam is a python module for reading and manipulating files in the SAM/BAM format. The SAM/BAM format is a way to store efficiently large numbers of alignments (Li 2009), such as those routinely created by next-generation sequencing methods. Pysam is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. Original-Maintainer: Andreas Heger Package: python3-statsmodels Version: 0.9.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: cython3 (>= 0.23), python3, python3-numpy (>= 1.11), python3-pandas (>= 0.14), python3-patsy (>= 0.3.0), python3-scipy (>= 0.14) Recommends: python3-matplotlib (>= 1.3) Suggests: python3-sphinx (>= 1.3), python3-nose (>= 1.3), ipython3 (>= 2.4) Filename: ./python3-statsmodels_0.9.0-0lbi_amd64.deb Size: 10201108 MD5sum: 40131cdff0b9593357570434192083b3 SHA1: d825ccd4dc4bd8c9cda6d491823b507d34039e0d SHA256: 08d4fb508ed548746e1bc339ebc7665157d76ce0a48559ab4470aff6944ad01c Section: science Priority: optional Homepage: http://www.statsmodels.org/ Description: statistical modeling and econometrics in Python Statsmodels is a Python package that provides a complement to scipy for statistical computations including descriptive statistics and estimation and inference for statistical models. Original-Maintainer: Josef Perktold Package: python3-tqdm Version: 4.61.2-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: python3:any Filename: ./python3-tqdm_4.61.2-0lbi_all.deb Size: 85092 MD5sum: 1d269a7ebffb5df6cb90b9b491c8052e SHA1: a45f13acdbe5d58d09d3d3488e19eaa749c4ba2a SHA256: f033760881e8650e8d8a9607341c127c37d2a04e9f39c36c62fd9206dc2274b3 Section: python Priority: optional Homepage: https://tqdm.github.io Description: Fast, Extensible Progress Meter tqdm derives from the Arabic word "taqaddum" (تقدّم) which can mean "progress", and is an abbreviation for "I love you so much" in Spanish ("te quiero demasiado"). . Instantly make your loops show a smart progress meter - just wrap any iterable with "tqdm(iterable)", and you're done! Author: Sandro Tosi Original-Maintainer: tqdm developers Package: qtbase-abi-fake Version: 5.9.5-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Provides: qtbase-abi-5-9-5 Filename: ./qtbase-abi-fake_5.9.5-1lbi_all.deb Size: 920 MD5sum: 3827ed305488515c2df11df8c6554745 SHA1: 68d8c1971b5f0aa086d7a07be65e8bb96ccd33ea SHA256: 0497f99ad05e11e9a4bcc2b9b8ce0136fed8ef9ce26138090dcf74c9e12a2c5d Section: custom Priority: optional Description: Fakes out python-pyqt5 from Ubuntu 18.04 to work on 20.04 Package: quast Version: 5.0.2-5lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: perl (>= 5.6.0), python3 (>= 3.3), python3-joblib, python3-simplejson, zlib1g-dev Recommends: default-jre (>= 1.8), libfreetype6-dev, libpng-dev, libtime-hires-perl, python3-matplotlib (>= 1.1), r-base-core Filename: ./quast_5.0.2-5lbi_amd64.deb Size: 11306528 MD5sum: 3a0e27e030f18fd4c66ca17ece85e06f SHA1: 26d54c1e49a7d7ae684482ee2c7181f2dfcf8cd9 SHA256: 3b74fa5a0f83c1c631adbc7538e8296a36618bf0d3560d8466c6351d1f555b83 Section: misc Priority: optional Homepage: http://quast.sf.net Description: Genome assembly evaluation tool QUAST evaluates genome assemblies. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Original-Maintainer: QUAST Support Package: r-bioc-annotationhub Version: 2.4.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-annotationdbi (>= 1.31.19), r-bioc-biobase, r-bioc-biocgenerics (>= 0.15.10), r-bioc-biocinstaller, r-bioc-interactivedisplaybase, r-bioc-s4vectors, r-cran-httr Filename: ./r-bioc-annotationhub_2.4.2-0lbi_amd64.deb Size: 378304 MD5sum: fcd6af57ea62863c204548a04354349e SHA1: 75f5b312d9ac6d0c7109eb8d1bcaa989e2ff2276 SHA256: 29eb5e6e78a343c2a9a1df7d07d70e79523a338726badd1652d384d13c7abcf5 Section: gnu-r Priority: optional Description: Client to access AnnotationHub resources This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access. Original-Maintainer: Bioconductor Package Maintainer Package: r-bioc-biocparallel Version: 1.24.1-0lbi Architecture: amd64 Maintainer: Labortório de Bioinformática Depends: r-base-core (>= 4.0), r-cran-futile.logger, r-cran-snow Filename: ./r-bioc-biocparallel_1.24.1-0lbi_amd64.deb Size: 1573368 MD5sum: 5f5f02f9616e4a669c7ebfa0747a6622 SHA1: e9670229a47155254110552093ee668dfa83436e SHA256: b80f1ebe0bf5af04bbba6ecff4aef43dec4221b1622dc3429a7072129d459b8a Section: gnu-r Priority: optional Homepage: https://github.com/Bioconductor/BiocParallel Description: Bioconductor facilities for parallel evaluation This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects. Author: Michel Lang , Ryan Thompson Original-Maintainer: Bioconductor Package Maintainer Package: r-bioc-biovizbase Version: 1.20.0-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.10), r-bioc-annotationdbi, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-ensembldb (>= 1.3.8), r-bioc-genomicalignments (>= 1.1.16), r-bioc-genomicfeatures (>= 1.21.19), r-bioc-genomicranges (>= 1.23.21), r-bioc-rsamtools (>= 1.17.28), r-bioc-variantannotation (>= 1.11.4), r-cran-hmisc, r-cran-scales Filename: ./r-bioc-biovizbase_1.20.0-1lbi_amd64.deb Size: 2512364 MD5sum: cd049cbfcdd529f244ca3e94111d6cd8 SHA1: 8a5d328cbcc71e07359bc846eb81bdc850ff6646 SHA256: 27cc2a25fff44a16e51120af07e8d3a5e9f0832e7374e8d8f3471640edf8a3b1 Section: gnu-r Priority: optional Homepage: http://bioconductor.org/packages/release/bioc/html/biovizBase.html Description: Basic graphic utilities for visualization of genomic data The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency. Original-Maintainer: Michael Lawrence Package: r-bioc-bsgenome Version: 1.40.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.8.0), r-bioc-biobase, r-bioc-biocgenerics (>= 0.13.8), r-bioc-rtracklayer (>= 1.25.8) Filename: ./r-bioc-bsgenome_1.40.1-0lbi_amd64.deb Size: 6425226 MD5sum: 528ab0a6bb0f69063e1d21da20ee3393 SHA1: d688d12063bf3ffcc9ec6fc2054527d76e804c2a SHA256: fcc5f8bc2502b33a06cfe766a5af5406aa7d8f475b15807a0285a81f9f6e5593 Section: gnu-r Priority: optional Homepage: http://bioconductor.org/packages/release/bioc/html/BSgenome.html Description: Infrastructure for Biostrings-based genome data packages Infrastructure shared by all the Biostrings-based genome data packages. Original-Maintainer: H. Pagès Package: r-bioc-dada2 Version: 1.10.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 3.2.0), r-bioc-biobase, r-bioc-biocgenerics (>= 0.28.0), r-bioc-biostrings (>= 2.42.1), r-bioc-iranges (>= 2.6.0), r-bioc-shortread (>= 1.32.0), r-bioc-xvector (>= 0.16.0), r-cran-data.table (>= 1.9.4), r-cran-ggplot2 (>= 2.1.0), r-cran-rcpp (>= 0.11.2), r-cran-rcppparallel (>= 4.3.0), r-cran-reshape2 (>= 1.4.1) Suggests: r-cran-knitr, r-cran-rmarkdown Filename: ./r-bioc-dada2_1.10.1-0lbi_amd64.deb Size: 3563324 MD5sum: c09cd67250b26e25ab71959a1da9c87c SHA1: 12be820ce1297ece8aec3bb65b3cf6391d7ea059 SHA256: 5f175521e977357c3b2e9e0e777d1017e005feee42f6c9f2ef08b1472f8f3088 Section: gnu-r Priority: optional Homepage: http://benjjneb.github.io/dada2/ Description: Sample inference from amplicon sequencing data The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching. Author: Benjamin Callahan, Paul McMurdie, Susan Holmes Original-Maintainer: Benjamin Callahan Package: r-bioc-delayedarray Version: 0.16.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 3.4), r-bioc-biobase, r-bioc-biocgenerics (>= 0.31.5), r-bioc-iranges (>= 2.17.3), r-bioc-matrixgenerics (>= 1.1.3), r-bioc-s4vectors (>= 0.26.1), r-cran-matrix Filename: ./r-bioc-delayedarray_0.16.0-0lbi_amd64.deb Size: 2023132 MD5sum: 3f2ef9ef010742ccf19be3c7bdb99753 SHA1: 21c2bae262d91995286f281723d2af2579d78ca0 SHA256: 24269d636f5210a350bccf23bf2c1b8c6aafb67af316b4fb1afef244692f2449 Section: gnu-r Priority: optional Homepage: https://bioconductor.org/packages/DelayedArray Description: Working transparently with on-disk and in-memory array-like datasets Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames. Author: Peter Hickey Original-Maintainer: Hervé Pagès Package: r-bioc-deseq2 Version: 1.30.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics (>= 0.7.5), r-bioc-biocparallel, r-bioc-genefilter, r-bioc-geneplotter, r-bioc-genomicranges, r-bioc-iranges, r-bioc-s4vectors (>= 0.23.18), r-bioc-summarizedexperiment (>= 1.1.6), r-cran-ggplot2, r-cran-rcpp (>= 0.11.0) Filename: ./r-bioc-deseq2_1.30.0-0lbi_amd64.deb Size: 3460972 MD5sum: 1889745311dee9d5733849c9b1a5e840 SHA1: a492de9cf21722c0099b72ad25edd0e8199455d6 SHA256: 5cd0e3dd6e0590045ea8bd32dd5d214981ce8e8d25fb2eb0cde167565da08f63 Section: science Priority: optional Homepage: https://github.com/mikelove/DESeq2 Description: Differential gene expression analysis based on the negative binomial distribution Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Original-Maintainer: Michael Love Package: r-bioc-dexseq Version: 1.18.4-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-biomart, r-bioc-deseq2 (>= 1.9.11), r-bioc-genefilter, r-bioc-geneplotter, r-bioc-genomicranges (>= 1.23.7), r-bioc-iranges (>= 2.5.17), r-bioc-rsamtools, r-cran-hwriter, r-cran-rcolorbrewer, r-cran-statmod, r-cran-stringr Suggests: r-bioc-genomicfeatures (>= 1.13.29), r-cran-knitr Filename: ./r-bioc-dexseq_1.18.4-0lbi_all.deb Size: 537866 MD5sum: 82fb37b3113cd4ceca72176a9cff6252 SHA1: 18bcf098d3866439941774231bf1cb6e18de1d21 SHA256: d88d715ce499b9647c1cfced5ab1019f45ffcb982a20d1c45988d592c4e7796d Section: gnu-r Priority: optional Description: Inference of differential exon usage in RNA-Seq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. Author: Simon Anders , Alejandro Reyes Original-Maintainer: Alejandro Reyes Package: r-bioc-ensembldb Version: 1.4.7-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-annotationdbi (>= 1.31.19), r-bioc-annotationhub, r-bioc-biobase, r-bioc-biocgenerics (>= 0.15.10), r-bioc-genomicfeatures (>= 1.23.18), r-bioc-s4vectors Filename: ./r-bioc-ensembldb_1.4.7-0lbi_amd64.deb Size: 1005290 MD5sum: 2b8808d7775c74ed90c3e4a99f1d76de SHA1: dfc7ef85bdc589062c55b6050790a30898d9be66 SHA256: cd75ee96ea500e4dd655f908ef034b50ac7a9db0b367f6d0a52c48d4e659aaff Section: gnu-r Priority: optional Homepage: https://github.com/jotsetung/ensembldb Description: Utilities to create and use an Ensembl based annotation database The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. Original-Maintainer: Johannes Rainer Package: r-bioc-fastseg Version: 1.32.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-iranges, r-bioc-s4vectors Filename: ./r-bioc-fastseg_1.32.0-0lbi_amd64.deb Size: 465580 MD5sum: a28089be9ae02b2720f2d4d049bc1f9d SHA1: be5311d8287c0fec0801c3f047f74d4b389f5b69 SHA256: 706711de8069fda2c5abe5a38beddcf06b08ed9636eb34050ecb03037e1771dd Section: gnu-r Priority: optional Homepage: http://www.bioinf.jku.at/software/fastseg/fastseg.html Description: fastseg - a fast segmentation algorithm fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments' first and higher order moments. Author: Guenter Klambauer Original-Maintainer: Guenter Klambauer Package: r-bioc-geneplotter Version: 1.68.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-annotate, r-bioc-annotationdbi, r-bioc-biobase, r-bioc-biocgenerics, r-cran-lattice, r-cran-rcolorbrewer Filename: ./r-bioc-geneplotter_1.68.0-0lbi_all.deb Size: 1554408 MD5sum: dca05cc33fed529e9581f834ae061f2b SHA1: 05b9011a5e476f71fde121716d2b86515518bc65 SHA256: 2f4f56dc324f5216d1a78f1a66ac6bd0a25a6c0fff7ec59f7d601c2166969209 Section: gnu-r Priority: optional Homepage: https://bioconductor.org/packages/geneplotter/ Description: Graphics related functions for Bioconductor Functions for plotting genomic data Original-Maintainer: Bioconductor Package Maintainer Package: r-bioc-genomicfeatures Version: 1.24.5-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-annotationdbi (>= 1.33.15), r-bioc-biobase (>= 2.15.1), r-bioc-biocgenerics (>= 0.1.0), r-bioc-biomart (>= 2.17.1), r-bioc-rtracklayer (>= 1.29.24) Filename: ./r-bioc-genomicfeatures_1.24.5-0lbi_all.deb Size: 1043910 MD5sum: 47038c7fc44c3bf2a8b889a09f599140 SHA1: 4644a56b38ee4ab298990a34b42fa4177256e53f SHA256: 5e5b6566d45cfd2c9ebb281458bfd16afc6ec4c3cfd48268283dc627c9e2802c Section: gnu-r Priority: optional Homepage: http://www.bioconductor.org/packages/release/bioc/html/GenomicFeatures.html Description: Tools for making and manipulating transcript centric annotations A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format. Original-Maintainer: Bioconductor Package Maintainer Package: r-bioc-genomicranges Version: 1.40.0+really1.38.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-genomeinfodb (>= 1.15.2), r-bioc-iranges (>= 2.19.9), r-bioc-s4vectors (>= 0.23.19), r-bioc-xvector (>= 0.19.8) Filename: ./r-bioc-genomicranges_1.40.0+really1.38.0-0lbi_all.deb Size: 2056640 MD5sum: 3275b44a7b5d96b187c1e188b07c454a SHA1: 5d4b5a5d0d3d9584b9aa2d0120b5ea18091d03e7 SHA256: 21bc300fb308285cbad531d1f0c11a0b045d95e523384499b27afbd2e6146c93 Section: gnu-r Priority: optional Description: Representation and manipulation of genomic intervals The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure. Original-Maintainer: Bioconductor Package Maintainer Package: r-bioc-gviz Version: 1.16.4-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.10.0), r-bioc-annotationdbi (>= 1.27.5), r-bioc-biobase (>= 2.15.3), r-bioc-biocgenerics (>= 0.11.3), r-bioc-biovizbase (>= 1.13.8), r-bioc-bsgenome (>= 1.33.1), r-bioc-rtracklayer (>= 1.25.13), r-cran-digest(>= 0.6.8), r-cran-latticeextra (>= 0.6), r-cran-matrixstats (>= 0.8.14) Filename: ./r-bioc-gviz_1.16.4-0lbi_all.deb Size: 4037652 MD5sum: d76560477d916aef0b978379fb1a2b81 SHA1: 85bc8da44d07c54e1d99229a9a9ee705a5df71d1 SHA256: d5832bc56b98a036d2d3b0b03cf82df1bed465a95917e9657012338675e8dba5 Section: gnu-r Priority: optional Description: Plotting data and annotation information along genomic coordinates Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Original-Maintainer: Florian Hahne Package: r-bioc-interactivedisplaybase Version: 1.10.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.10), r-bioc-biobase, r-bioc-biocgenerics, r-cran-shiny Filename: ./r-bioc-interactivedisplaybase_1.10.3-0lbi_amd64.deb Size: 31108 MD5sum: b8953019b610011845c89cabd4a613c2 SHA1: 5099ad57a7afae19e7ddabccb743bc32390e3146 SHA256: 88f61826306361517ce7a9d92a86b329c005d37083441ade03301fe327d1bd7b Section: gnu-r Priority: optional Description: Powerful shiny web displays of Bioconductor objects The interactiveDisplayBase package contains the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects. Original-Maintainer: Shawn Balcome Package: r-bioc-matrixgenerics Version: 1.2.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics, r-cran-matrixstats (>= 0.57.0) Filename: ./r-bioc-matrixgenerics_1.2.0-0lbi_all.deb Size: 280972 MD5sum: ff54f2e1551c0b946d65a2409a65bbbd SHA1: c37b9b7830ee061a8f6ee830eb068e65b19b83ef SHA256: 9425565ad2827544c11112d348d827716f3ab1e0e9d285082643905245477225 Section: gnu-r Priority: optional Homepage: https://bioconductor.org/packages/MatrixGenerics Description: S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities. Author: Constantin Ahlmann-Eltze , Hervé Pagès Original-Maintainer: Peter Hickey Package: r-bioc-methylkit Version: 1.15.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 3.5.0), r-bioc-biobase, r-bioc-biocgenerics, r-bioc-delayedarray, r-bioc-fastseg, r-bioc-genomeinfodb, r-bioc-genomicranges (>= 1.18.1), r-bioc-iranges, r-bioc-limma, r-bioc-qvalue, r-bioc-rsamtools, r-bioc-rtracklayer, r-bioc-s4vectors (>= 0.13.13), r-cran-data.table (>= 1.9.6), r-cran-emdbook, r-cran-gridbase, r-cran-gtools, r-cran-kernsmooth, r-cran-mclust, r-cran-mgcv, r-cran-rcpp, r-cran-r.utils Filename: ./r-bioc-methylkit_1.15.3-0lbi_amd64.deb Size: 2353400 MD5sum: 21fb223171a93692acbdb489d06f0eca SHA1: 6c4fa62c824b2c88538ba2a3cba54fb88d5aa720 SHA256: a679363af5db65097e7a0a2a545f026e16e292a798e20cb418798e4eb1cf9ed9 Section: gnu-r Priority: optional Homepage: https://github.com/al2na/methylKit Description: DNA methylation analysis from high-throughput bisulfite sequencing results methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files. Author: Alexander Gosdschan Original-Maintainer: Altuna Akalin Package: r-bioc-mgsa Version: 1.20.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.14.0), r-bioc-biobase, r-bioc-biocgenerics, r-cran-gplots Suggests: r-bioc-go.db, r-cran-dbi, r-cran-rsqlite, r-cran-testthat Filename: ./r-bioc-mgsa_1.20.0-0lbi_amd64.deb Size: 428394 MD5sum: 24ed75660d105d67108688fbcfefe065 SHA1: c03c64a2f6512470aa5ac24288731d1101a9e60e SHA256: a048a147270233b0db2294865f6567cd0f24e1ff79453e1b91395536d6c547c4 Section: gnu-r Priority: optional Description: Model-based gene set analysis Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology. Author: Sebastian Bauer , Julien Gagneur Original-Maintainer: Sebastian Bauer Package: r-bioc-org.mm.eg.db Version: 3.3.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.7.0), r-bioc-annotationdbi (>= 1.33.10), r-bioc-biobase, r-bioc-biocgenerics Suggests: r-bioc-annotate, r-cran-runit Filename: ./r-bioc-org.mm.eg.db_3.3.0-0lbi_all.deb Size: 28596858 MD5sum: 737cb727668b41cff1b312d19cdcc8fe SHA1: 82746d602ca073f320af399c469fbc86afbecaf2 SHA256: 747603281f81e0f1acb6df331fae481b03fd4d18fee643408236ccc904f43602 Section: gnu-r Priority: optional Description: Genome wide annotation for Mouse Genome wide annotation for Mouse, primarily based on mapping using Entrez Gene identifiers. Author: Marc Carlson Original-Maintainer: Bioconductor Package Maintainer Package: r-bioc-qvalue Source: qvalue Version: 1:1.38.0-0biolinux1 Architecture: all Maintainer: cran2deb4ubuntu Installed-Size: 320 Depends: r-base-core (>= 3.0) Conflicts: r-cran-qvalue Replaces: r-cran-qvalue Provides: r-cran-qvalue Filename: ./r-bioc-qvalue_1:1.38.0-0biolinux1_all.deb Size: 218808 MD5sum: f7707f6087cd3011c3696677e8b6cc69 SHA1: 3cc02a474a031002bc6ed543d44f4a8bef14b227 SHA256: 9d331592ffb4f1909f45fd5d57c139b297d978b760b934e687db29d5781c4208 Section: gnu-r Priority: optional Description: Bioconductor package "Q-value estimation for false discovery rate control" This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. . This package used to be in CRAN but is now in Bioconductor. . Author: Alan Dabney and John D. Storey , with assistance from Gregory R. Warnes . Maintainer: John D. Storey Package: r-bioc-reactome.db Version: 1.55.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.7.0), r-bioc-annotationdbi (>= 1.33.0), r-bioc-biobase, r-bioc-biocgenerics Filename: ./r-bioc-reactome.db_1.55.0-0lbi_all.deb Size: 238996342 MD5sum: a73282c69d064744e8ed2f4cdf5c6f8e SHA1: ba61aa97be8b14284b4262665b718a8c7d3e5b16 SHA256: 4f3956b1da2c6aea365ff4bfe5fc8cc08f01431bc0e8550b08139faf13a4c84f Section: gnu-r Priority: optional Description: A set of annotation maps for reactome A set of annotation maps for reactome assembled using data from reactome. Author: Willem Ligtenberg Original-Maintainer: Willem Ligtenberg Package: r-bioc-reportingtools Version: 2.20.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics, r-cran-knitr Filename: ./r-bioc-reportingtools_2.20.0-0lbi_all.deb Size: 1935322 MD5sum: d21ae2a31a9d6307336d1b82951fc7a5 SHA1: 3cbf6c7d1d1281f94d052646de842959376900d2 SHA256: 139c389a002c280f8c9eddaa9c90483132f5436161e64abaa0a99823732ae7af Section: gnu-r Priority: optional Description: Tools for making reports in various formats The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. Original-Maintainer: Jason A. Hackney , Gabriel Becker , Jessica L. Larson Package: r-bioc-rhdf5 Version: 2.14.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics Filename: ./r-bioc-rhdf5_2.14.0-0lbi_amd64.deb Size: 1377028 MD5sum: f38b59173a038aacbc453fcabe5c94c7 SHA1: 5ab3a24010b3586d3ee2d20f61af94f780cbe8ef SHA256: e3fd2a774d8f663c74c9900dad75abe65b79332039b4e72021b90ba3d8c643ab Section: gnu-r Priority: optional Description: HDF5 interface to R This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM. Author: Bernd Fischer, Gregoire Pau Original-Maintainer: Bernd Fischer Package: r-bioc-rhtslib Version: 1.18.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libcurl-dev, libbz2-dev, liblzma-dev, r-base-core, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-zlibbioc Filename: ./r-bioc-rhtslib_1.18.1-0lbi_amd64.deb Size: 2416284 MD5sum: 806bf47b0b762ceef8a0b669024063ee SHA1: 83f7387fc06012a577e6eed6cd5fa58c2d3786f0 SHA256: b01cd73d9e0497fe49ae37226838e0230cf880f1798dd6b5cd3e2fdd6a17f673 Section: gnu-r Priority: optional Homepage: https://github.com/Bioconductor/Rhtslib Description: HTSlib high-throughput sequencing library This package provides version 1.7 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R Author: Martin Morgan Original-Maintainer: Nathaniel Hayden Package: r-bioc-rsubread Version: 2.8.1-2 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 35101 Depends: r-base-core (>= 4.1.2-1ubuntu1), r-api-4.0, r-api-bioc-3.14 | r-bioc-biocgenerics, r-cran-matrix, libc6 (>= 2.34), zlib1g (>= 1:1.2.2.4) Filename: ./r-bioc-rsubread_2.8.1-2_amd64.deb Size: 8165128 MD5sum: d058fb7503fbf0ca149ca0e043610263 SHA1: a8792047d54ec6d41d53a11772c777bf370850f3 SHA256: a594f115baca1de0c067735fdedfdfe41f46dd24f66b721fe4b0af074dd3193c Section: gnu-r Priority: optional Homepage: https://bioconductor.org/packages/Rsubread/ Description: Subread Sequence Alignment and Counting for R Alignment, quantification and analysis of second and third generation sequencing data. Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. . Can be applied to all major sequencing techologies and to both short and long sequence reads. Original-Maintainer: Debian R Packages Maintainers Package: r-bioc-sleuth Version: 0.28.1-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 3.2.1), r-bioc-biobase, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-rhdf5, r-cran-assertthat, r-cran-bh, r-cran-data.table, r-cran-dbi, r-cran-ggplot2, r-cran-shiny, r-cran-tidyr Filename: ./r-bioc-sleuth_0.28.1-1lbi_amd64.deb Size: 4810930 MD5sum: f1475d2a207dbac9757a7fdf361e5bd9 SHA1: 82b7aad85f23a5192fe6d2dd159a0929559807b9 SHA256: 510257303980baffd79f890874d136017b9731db12c93098b431ed82d8ccf019 Section: gnu-r Priority: optional Description: Tools for investigating RNA-Seq Investigate transcript abundance from "kallisto" and differential expression analysis from RNA-Seq data. Author: Harold Pimentel Original-Maintainer: Harold Pimentel Package: r-bioc-sparsearray Version: 1.6.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-s4arrays Filename: ./r-bioc-sparsearray_1.6.2-0lbi_amd64.deb Size: 1981510 MD5sum: 4167018b8609a665f08c6123d71e2907 SHA1: 7be05c30f4dba330de924a1c0d3cb1d739f1eb42 SHA256: 6139697038c707da5cafc1d0d8ef73232da35ae162b07f2da6736b89c22adb83 Section: gnu-r Priority: optional Homepage: https://bioconductor.org/packages/SparseArray Description: High-performance sparse data representation and manipulation in R The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, They suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN. Author: Hervé Pagès Original-Maintainer: Bioconductor Package Maintainer Package: r-bioc-sradb Version: 1.34.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-geoquery, r-bioc-graph, r-cran-rcurl, r-cran-rsqlite Suggests: r-bioc-rgraphviz Filename: ./r-bioc-sradb_1.34.0-0lbi_all.deb Size: 388276 MD5sum: 5e22922caff9ecc09d51f7ac7ce6398c SHA1: 3dc6f5d693e31e623c89e3c87f29508a2dd0eec8 SHA256: d8f805ee561f1bcf4f8a1dc2be4e11e2be8d5a5306849402bc259245487546bb Section: gnu-r Priority: optional Description: A compilation of metadata from NCBI SRA and tools The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. . SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata. Author: Jack Zhu and Sean Davis Original-Maintainer: Jack Zhu Package: r-bioc-summarizedexperiment Version: 1.20.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 3.2), r-bioc-biobase, r-bioc-biocgenerics (>= 0.15.3), r-bioc-delayedarray (>= 0.15.10), r-bioc-genomeinfodb (>= 1.13.1), r-bioc-genomicranges (>= 1.40.0), r-bioc-iranges (>= 2.22.2), r-bioc-matrixgenerics (>= 1.1.3), r-bioc-s4vectors (>= 0.26.1), r-cran-matrix Filename: ./r-bioc-summarizedexperiment_1.20.0-0lbi_all.deb Size: 2183920 MD5sum: 0b536b050ec26b78d92c9f2e22d6253d SHA1: 7e59806965bbc18377f96a1c519cacd4a71a9276 SHA256: adc16363a99a2f99372cee343efd657bcb3c4daddd88a11b324a715871bd5cbe Section: gnu-r Priority: optional Homepage: https://bioconductor.org/packages/SummarizedExperiment/ Description: BioConductor assay container The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples. Original-Maintainer: Bioconductor Package Maintainer Package: r-bioc-variantannotation Version: 1.18.6-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.8.0), r-bioc-annotationdbi (>= 1.27.9), r-bioc-biobase, r-bioc-biocgenerics (>= 0.15.3), r-bioc-bsgenome (>= 1.37.6), r-bioc-genomicfeatures (>= 1.19.17), r-bioc-rtracklayer (>= 1.25.16) Filename: ./r-bioc-variantannotation_1.18.6-0lbi_amd64.deb Size: 2221794 MD5sum: 4617ef25e00a3625ce838579aa590f16 SHA1: c8d49cf3ee535e27c255fd4c8cabb0f1f813087f SHA256: ca3f6a317e1bb305fe62b7cc98569b5197bf497a991e67766d6e62dfb2540f07 Section: gnu-r Priority: optional Description: Annotation of Genetic Variants Annotate variants, compute amino acid coding changes, predict coding outcomes. Original-Maintainer: Valerie Obenchain Package: r-bioc-venndiagram Version: 1.6.17-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 2.14.1), r-bioc-biocgenerics, r-bioc-biobase, r-cran-futile.logger Suggests: r-cran-testthat Filename: ./r-bioc-venndiagram_1.6.17-0lbi_all.deb Size: 125872 MD5sum: 3430bcd4d18bc7f463bce130fc1bbfc6 SHA1: 94da31c24e970707ef6d2a3527728e966a0f4b71 SHA256: 33dc2635793b056e5cbc360fe8268fd871fa4b62eb49f6cc0a2dba860410a17f Section: gnu-r Priority: optional Description: Generate High-Resolution Venn and Euler Plots A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. . Author: Hanbo Chen Original-Maintainer: Paul Boutros Package: r-boutroslab-plotting-general Version: 5.3.4-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 3.0.2), r-cran-cluster (>= 1.14.4), r-cran-hexbin (>= 1.26.3), r-cran-lattice (>= 0.20), r-cran-latticeextra (>= 0.6), r-cran-mass (>= 7.3) Filename: ./r-boutroslab-plotting-general_5.3.4-0lbi_amd64.deb Size: 2486370 MD5sum: 340588385d7448d411e94d356762ea88 SHA1: 1ea89f812fa67d5543e4ba7176ba12b73148a5f0 SHA256: 2106f7a0c6a281cab9413f19ec71354980858456ba356fdfaed8ef7b64191798 Section: gnu-r Priority: optional Description: BoutrosLab Plotting General Scientific research is filled with complex datasets which may be understood and communicated using data visualization techniques. The BoutrosLab.plotting.general (BPG) package creates publication-ready figures which are reproduceable, highly customizable, and useful for both interim analysis and communication of data. Original-Maintainer: Paul Boutros Package: r-cran-biganalytics Source: biganalytics Version: 1.1.14-1cran2ppa2 Architecture: amd64 Maintainer: cran2deb4ubuntu Installed-Size: 260 Depends: r-base-core, r-cran-bigmemory, r-cran-foreach, r-cran-biglm, r-cran-rcpp, r-cran-bh, libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 4.1.1) Filename: ./third-party/r-cran-biganalytics_1.1.14-1cran2ppa2_amd64.deb Size: 105256 MD5sum: e0289b3a4060f80bdc1280e256aac3d4 SHA1: f31be6d9f9755940b93754bf78b192bd70e380f5 SHA256: 929fd7c08ea9a8eaffd0e3df528820ef1aa0ab4d122b7d66baabd853de4aecc7 Section: gnu-r Priority: optional Homepage: http://www.bigmemory.org Description: GNU R package "Utilities for 'big.matrix' Objects from Package 'bigmemory'" . Extend the 'bigmemory' package with various analytics. Functions 'bigkmeans' and 'binit' may also be used with native R objects. For 'tapply'-like functions, the bigtabulate package may also be helpful. For linear algebra support, see 'bigalgebra'. For mutex (locking) support for advanced shared-memory usage, see 'synchronicity'. . Author: John W. Emerson and Michael J. Kane . Maintainer: Michael J. Kane . (Repackaged on Tue, 06 Nov 2018 13:59:42 -0200 by dpkg-repack.) Package: r-cran-biotools Version: 3.1-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-cran-deldir, r-cran-gdata, r-cran-gmodels, r-cran-lattice, r-cran-learnbayes, r-cran-maptools, r-cran-mass, r-cran-raster, r-cran-rpanel, r-cran-sf, r-cran-spatialepi, r-cran-spdata, r-cran-spdep, r-cran-tkrplot, r-cran-units Filename: ./r-cran-biotools_3.1-0lbi_all.deb Size: 444572 MD5sum: 092defe2a9618dc4b12e3221643c376c SHA1: bc1389a67e6ac3507399384fcf35d50913dd3b6e SHA256: 1313447cc37e0b3b898640e7cbcc692e6208f83b10d7aae5c969ca70446d2e03 Section: gnu-r Priority: optional Description: Tools for Biometry and Applied Statistics in Agricultural Science Tools designed to perform and work with cluster analysis (including Tocher's algorithm), discriminant analysis and path analysis (standard and under collinearity), as well as some useful miscellaneous tools for dealing with sample size and optimum plot size calculations. Mantel's permutation test can be found in this package. A new approach for calculating its power is implemented. biotools also contains the new tests for genetic covariance components. An approach for predicting spatial gene diversity is implemented. Original-Maintainer: Anderson Rodrigo da Silva Package: r-cran-compositions Source: compositions Version: 2.0-4-1cran1.2004.0 Architecture: amd64 Maintainer: cran2deb4ubuntu Installed-Size: 2382 Depends: r-cran-rcpp, r-base-core, r-cran-tensora, r-cran-robustbase, r-cran-bayesm, r-cran-mass, libblas3 | libblas.so.3, libc6 (>= 2.29), liblapack3 | liblapack.so.3 Filename: ./third-party/r-cran-compositions_2.0-4-1cran1.2004.0_amd64.deb Size: 1895788 MD5sum: 1d2bbd6dceba2684a8e42c9f4ad9433e SHA1: c76f958e5130898bf6e2a6a091fee08def214b85 SHA256: 5e8fd2cf4628edfff781a56c4627881f3f229351e833d9571543315e9a0f930e Section: gnu-r Priority: optional Homepage: http://www.stat.boogaart.de/compositions/ Description: GNU R package "Compositional Data Analysis" . Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn. . Author: K. Gerald van den Boogaart , Raimon Tolosana-Delgado, Matevz Bren . Maintainer: K. Gerald van den Boogaart . (Repackaged on Mon, 02 May 2022 16:20:05 -0300 by dpkg-repack.) Package: r-cran-factoextra Version: 1.0.5-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base (>= 3.1.2), r-cran-abind, r-cran-factominer, r-cran-ggplot2 (>= 2.2.0), r-cran-cluster, r-cran-dendextend, r-cran-ggpubr (>= 0.1.5), r-cran-ggrepel, r-cran-reshape2, r-cran-tidyr Filename: ./r-cran-factoextra_1.0.5-1lbi_amd64.deb Size: 488908 MD5sum: ba69daaff379ab6d56301b3bda90c166 SHA1: e0186d0208e1830a72a5229f54db43df6c604f7a SHA256: 5e51324d45f853b9db465acb5fd17cee3213f13e359109fb38c1a5f4a21da6d1 Section: gnu-r Priority: optional Description: Extract and Visualize the Results of Multivariate Data Analyses Provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides 'ggplot2' - based elegant data visualization. Author: Alboukadel Kassambara, Fabian Mundt Original-Maintainer: Alboukadel Kassambara Package: r-cran-harmony Version: 1.2.4-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-cran-rcpp, r-cran-rcpparmadillo, r-cran-rcppprogress, r-cran-rhpcblasctl Filename: ./r-cran-harmony_1.2.4-0lbi_all.deb Size: 7399342 MD5sum: f4adb82d3ba21a315a0c21f11a8f2250 SHA1: f371fce99ba560348be156f4d3308269c5a73e32 SHA256: 7a47af7d7481601ee8b72087bb568b1ec631c6d4ba45a2c8e346b4cedc0cd960 Section: gnu-r Priority: optional Homepage: https://github.com/immunogenomics/harmony Description: Fast, Sensitive, and Accurate Integration of Single Cell Data Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al (doi:10.1038/s41592-019-0619-0). Package includes a standalone Harmony function and interfaces to external frameworks. Original-Maintainer: Ilya Korsunsky Package: r-cran-heatmaply Version: 0.15.2-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 3.0.0), r-cran-assertthat, r-cran-colorspace, r-cran-dendextend (>= 1.4.0), r-cran-gclus, r-cran-ggplot2 (>= 2.2.0), r-cran-gplots, r-cran-hexbin, r-cran-htmlwidgets, r-cran-magrittr (>= 1.0.1), r-cran-plotly (>= 4.7.1), r-cran-qap, r-cran-rcolorbrewer, r-cran-registry, r-cran-reshape2, r-cran-scales, r-cran-seriation, r-cran-tsp, r-cran-viridis, r-cran-webshot Filename: ./r-cran-heatmaply_0.15.2-1lbi_all.deb Size: 1438068 MD5sum: 19d531372d5d0100278cae362b8d9576 SHA1: 07731d2a0d508dea68114e24374d0e8dbb72dc48 SHA256: 6239216f556f712cac19f8d34c759b4db62ad6c75323130683d4d17a39dbc89b Section: gnu-r Priority: optional Homepage: https://cran.r-project.org/package=heatmaply Description: Interactive Cluster Heat Maps Using plotly Create interactive cluster heatmaps that can be saved as a standalone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. . Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the heatmap. Original-Maintainer: Tal Galili Package: r-cran-plnmodels Version: 0.9.1-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: libnlopt-dev, r-base-core (>= 3.4), r-bioc-biomformat, r-bioc-phyloseq, r-cran-corrplot, r-cran-dplyr, r-cran-ggplot2, r-cran-glassofast, r-cran-gridextra, r-cran-igraph, r-cran-magrittr, r-cran-mass, r-cran-matrix, r-cran-nloptr (>= 1.2.0), r-cran-r6, r-cran-rcpparmadillo, r-cran-tidyr Suggests: r-cran-ggally Filename: ./r-cran-plnmodels_0.9.1-1lbi_all.deb Size: 2169404 MD5sum: f74c473afcd59fc6be4caa36255b98f9 SHA1: 1a1a2b6b16d14a6c282078378a3b562c18335de6 SHA256: 9414fddc197ca2e62fbad132b90b014f59bbf64422d6043da7eda9a9e4c2ff08 Section: gnu-r Priority: optional Homepage: https://jchiquet.github.io/PLNmodels/ Description: Poisson Lognormal Models The Poisson-lognormal model and variants can be used for a variety of multivariate problems when count data are at play, including principal component analysis for count data, discriminant analysis and network inference. Implements variational algorithms to fit such models accompanied with a set of functions for visualization and diagnostic. Author: Mahendra Mariadassou , Stéphane Robin Original-Maintainer: Julien Chiquet Package: r-cran-upsetr Version: 1.3.3-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: r-base-core, r-cran-ggplot2, r-cran-gridextra, r-cran-plyr, r-cran-scales Suggests: r-cran-knitr Filename: ./r-cran-upsetr_1.3.3-0lbi_all.deb Size: 3574564 MD5sum: 70f00479a9fc539a4ad2a429fa3ff14d SHA1: 4492da0803b4863fca34859a02440282c5694951 SHA256: a2f8098acdaf72bd7a3dc90995f57e89a4a29f4775505b00dbbb1b9d10ab66be Section: gnu-r Priority: optional Description: Venn and Euler Diagrams for Visualizing Intersecting Sets Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks. Author: Jake Conway , Nils Gehlenborg Home: http://github.com/hms-dbmi/UpSetR Original-Maintainer: Jake Conway Package: r-cran-wgcna Version: 1.69-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: r-base-core (>= 3.0), r-bioc-annotationdbi, r-bioc-impute, r-bioc-go.db, r-bioc-preprocesscore, r-cran-doparallel, r-cran-dynamictreecut (>= 1.62), r-cran-fastcluster, r-cran-foreach, r-cran-hmisc, r-cran-matrixstats (>= 0.8.1), r-cran-rcpp (>= 1.0.5), r-cran-survival Filename: ./r-cran-wgcna_1.69-0lbi_amd64.deb Size: 4466644 MD5sum: 45f114e06affec1e346d4994174773f4 SHA1: bdcf8f6df6139e3e4d15d6719b41545dc16aeee5 SHA256: 2c3fc2062d8efc6dab4172014111b4a08d6d8e1890d1694edc7b8b60da37a705 Section: gnu-r Priority: optional Homepage: http://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ Description: Weighted correlation network analysis Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) and Langfelder and Horvath (2008) . Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization. Author: Peter Langfelder, Steve Horvath Original-Maintainer: Peter Langfelder Package: r-cran-zcompositions Source: zcompositions Version: 1.4.0-1-1cran1.2004.0 Architecture: all Maintainer: cran2deb4ubuntu Installed-Size: 338 Depends: r-base-core, r-cran-mass, r-cran-nada, r-cran-truncnorm Filename: ./third-party/r-cran-zcompositions_1.4.0-1-1cran1.2004.0_all.deb Size: 304696 MD5sum: 9bcefe58a458a8b39597baea0658a2b8 SHA1: 93448f2176267ffb33cfe0525dc4b2b48002ec2f SHA256: 275ed88115129a7a035ac735540384dcdc3e1c57efa0d2714405aa61ed9ea8ad Section: gnu-r Priority: optional Homepage: https://github.com/Japal/zCompositions Description: GNU R package "Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets" . Principled methods for the imputation of zeros, left-censored and missing data in compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) ). . Author: Javier Palarea-Albaladejo [cre, aut] (), Josep Antoni Martin-Fernandez [aut] () . Maintainer: Javier Palarea-Albaladejo . (Repackaged on Mon, 02 May 2022 16:20:11 -0300 by dpkg-repack.) Package: randfold Version: 2.0.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: biosquid Recommends: vienna-rna Filename: ./randfold_2.0.1-0lbi_amd64.deb Size: 43018 MD5sum: 1e871a5e6b4417bb0d38b25fb94e97cb SHA1: 7435328df5a6a8d1229cdbefd6f4c595664455c5 SHA256: 2f0d708e6190d4c79f66f70263b82559f4525f23621be834a69aa6d32a939942 Section: science Priority: optional Homepage: http://bioinformatics.psb.ugent.be/ Description: A randsomization test for sequence secondary structure RANDFOLD computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences. For more information, see the paper: Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics. 2004 Nov 22;20(17):2911-7 PMID: 15217813 Original-Maintainer: Eric Bonnet Package: rasdaemon Version: 0.6.6-3 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 294 Pre-Depends: init-system-helpers (>= 1.54~) Depends: libc6 (>= 2.14), libsqlite3-0 (>= 3.7.14), perl:any, sqlite3, libdbd-sqlite3-perl Filename: ./third-party/rasdaemon_0.6.6-3_amd64.deb Size: 83772 MD5sum: 37c08a7cdb0b28760e0776465bd9973f SHA1: 79e946b6b9b22c5cff9ce0c4d32fd34f2e11c2ca SHA256: fea6915b21219c158f0f1a46eda04eebace2c08e63092a212b4e74b8dc65ac9e Section: admin Priority: optional Homepage: https://github.com/mchehab/rasdaemon Description: utility to receive RAS error tracings rasdaemon is a RAS (Reliability, Availability and Serviceability) logging tool. It currently records memory errors, using the EDAC tracing events. EDAC are drivers in the Linux kernel that handle detection of ECC errors from memory controllers for most chipsets on x86 and ARM architectures. This userspace component consists of an init script which makes sure EDAC drivers and DIMM labels are loaded at system startup, as well as a utility for reporting current error counts from the EDAC sysfs files. Original-Maintainer: Debian QA Group Package: raxml Version: 8.2.12-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./raxml_8.2.12-0lbi_amd64.deb Size: 1385072 MD5sum: 5739c0d9d5ce0b68d2892fd3bd115774 SHA1: e61d68cd0967e95ae48af2c0c40924cbc06ea4c9 SHA256: 93aa212797e4f50d4ecda0a9f2b5d515e66c8a8dff1abdd5a4ebf5fcd7aac38f Section: science Priority: optional Homepage: http://sco.h-its.org/exelixis/web/software/raxml/ Description: Randomized Axelerated Maximum Likelihood RAxML is a program for sequential and parallel Maximum Likelihood-based inference of large phylogenetic trees. It has originally been derived from fastDNAml. . This package contains Hybrid MPI-Pthreads versions. Original-Maintainer: Alexandros Stamatakis Package: raxml-ng Version: 1.2.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bison, flex, libgmp3-dev Filename: ./raxml-ng_1.2.0-0lbi_amd64.deb Size: 1525942 MD5sum: 4fb06c2be8efc5d920e0af54b1da7789 SHA1: 117f78f1bab347baa08097739f3dac042b08c24e SHA256: fb48e8fa7183e8ced4b492d9f537b37d61d29201d56277569b94fffa77b346b6 Section: science Priority: optional Homepage: https://github.com/amkozlov/raxml-ng Description: RAxML Next Generation RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014). . RAxML-NG offers improvements in speed, flexibility and user-friendliness over the previous RAxML versions. It also implements some of the features previously available in ExaML (Kozlov et al. 2015), including checkpointing and efficient load balancing for partitioned alignments (Kobert et al. 2014). Original-Maintainer: Alexey Kozlov Package: rdp-classifier Version: 2.10.2+dfsg-0biolinux1 Architecture: all Maintainer: Steffen Moeller Installed-Size: 65580 Depends: libcommons-cli-java, librdp-readseq-java, librdp-taxonomy-tree-java, default-jre Recommends: rdp-classifier-doc Filename: ./rdp-classifier_2.10.2+dfsg-0biolinux1_all.deb Size: 13790372 MD5sum: 482591a28760a3412028e93c5075f4f2 SHA1: 3107f97c68b9ecae3a692e568c3734869579fe72 SHA256: f319dd096856e3190f9b1dcf3ef8e12e97654aa23a9dd504d66c0bb8bb11b315 Section: science Priority: extra Homepage: http://rdp.cme.msu.edu/. Description: taxonomic assignment from next generation sequencing The RDP Classifier is a nave Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. Package: rdp-classifier-doc Source: rdp-classifier Version: 2.10.2+dfsg-0biolinux1 Architecture: all Maintainer: Steffen Moeller Installed-Size: 3918 Suggests: rdp-classifier Filename: ./rdp-classifier-doc_2.10.2+dfsg-0biolinux1_all.deb Size: 259044 MD5sum: c0c292b8ce9f5275fece7d26f462f7fc SHA1: 1aadb28f828d51ad0aab1c9cd40579900bcd5563 SHA256: 7cf765eebe46ebd51dd2aa624319f1f45d83176e76259a17ca37772d696f2d0c Section: doc Priority: extra Homepage: http://rdp.cme.msu.edu/. Description: documentation and examples for rdp-classifier Includes the JavaDoc HTML Package: recycler Version: 0.62-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-networkx, python-nose, python-numpy, python-pysam Recommends: bwa (>= 0.7.5), samtools (>= 0.1.19), spades (>= 3.6.2) Filename: ./recycler_0.62-0lbi_amd64.deb Size: 19686 MD5sum: 16693dbb446498e3956c8ced2f9a9dad SHA1: 3bca81bf0efee893fcc50aa109ddf50032940793 SHA256: afda46b6be1ab48aa0035b6c0dbf47e0ab234644a9da503f76d24eb23daee27c Section: science Priority: optional Homepage: https://github.com/Shamir-Lab/Recycler Description: Detecting plasmids from de novo assembly graphs Recycler attempts to ameliorate plasmid extraction by introducing a new plasmid-specific assembly algorithm, leveraging assembly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assembled graph nodes. Recycler greatly increases the number of true plasmids recovered while remaining highly accurate. On simulated plasmidomes, Recycler recovered 5-14% more true plasmids compared to extant methods, and overall precision of about 90%. Original-Maintainer: Roye Rozov Package: repet Version: 2.5-9lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: awk, mysql-client (>= 5.5), ncbi-blast+, python2 (>= 2.6), python2 (<< 3), python-mysqldb, python-yaml Recommends: blast2, genometools, hmmer (>= 3), mcl, mreps, piler, repeatmasker (>= 3.2.5), repeatmasker-recon, trf (>= 4) Suggests: mafft, torque-client (>= 3.0.2) | gridengine-client (>= 6.1u5) Filename: ./repet_2.5-9lbi_amd64.deb Size: 6326608 MD5sum: 87309d501e3c0da76d9ffab5c7cd9e3f SHA1: 84ffb7a8cfc0c57aca1732091dfe1ea2248c8682 SHA256: 56169289d4b5c78f7598b6f99e33e1f67250f83c704bd975ba74390dd2e2455b Section: science Priority: optional Homepage: https://urgi.versailles.inra.fr/Tools/REPET Description: Pipelines to tackle biological issues The REPET package (Flutre et al, 2011) integrates bioinformatics programs in order to tackle biological issues at the genomic scale. * TEdenovo and TEannot pipeline for detection and annotation of transposable elements. * SegDup pipeline for segmental duplications. * SATannot pipeline for satellites. * Tallymer pipeline to get an overview of the amount and repartition of repetitions. Original-Maintainer: REPET Team Package: resfinder Version: 4.1.0-3lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: kma, ncbi-blast+, python3-biopython, python3-cgecore, python3-tabulate Filename: ./resfinder_4.1.0-3lbi_all.deb Size: 57136 MD5sum: 6fd65b408a8dc3d064a9578073ee071e SHA1: 53d5ba22107f4c02404ed06894bff94d27995e89 SHA256: 0c740105f86066a1f7b9ca7669cdd2bf707fd15b470d2c0ff41844013e329264 Section: science Priority: optional Homepage: https://bitbucket.org/genomicepidemiology/resfinder/ Description: Identification of antimicrobial resistance genes ResFinder identifies acquired antimicrobial resistance genes and/or chromosomal mutations in total or partial sequenced isolates of bacteria. Original-Maintainer: Carsten Friis , Mette Voldby Larsen Package: riborf Version: 2.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: perl Recommends: bowtie2, sra-toolkit, tophat Filename: ./riborf_2.0-0lbi_all.deb Size: 24148 MD5sum: c2ee1e4650ff77aa1d5aa57e4a07282b SHA1: ae3178288186583a7bb738be4c8d8c07138261fe SHA256: 6f271f2e7c5bcf455baa7142587bfd17e13a567199065b657aea7ad372a7988c Section: science Priority: optional Homepage: https://github.com/zhejilab/RibORF/ Description: Identifying genome-wide translated ORFs using ribosome profiling RibORF software (version 2.0) was originally published in (Ji et al., eLife, 2015). Compared to the version 1.0, we made some changes of the codes to improve the software performance. Original-Maintainer: Zhe Ji Package: ribowave Version: 1.0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: bedtools (>= 2.25.0), r-bioc-rhdf5, r-cran-ggplot2, r-cran-reshape, r-cran-wmtsa Filename: ./ribowave_1.0-1lbi_all.deb Size: 33070 MD5sum: 9e15d2cc7643863cee718697bb792baa SHA1: 591b4cd1c4f713af8e7a024aa185ba63d6009983 SHA256: 1deaaa1cc420a088a8e3a524c1dcaecdb6f70c2d0974ba3a6f433a6428c430c6 Section: science Priority: optional Homepage: https://github.com/lulab/Ribowave Description: Ribo-seq analysis tool RiboWave analyses Ribosome profiling data (Ribo-seq). It utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes (i.e. signal frequency) and precisely locate their footprint. . Translation is dynamically regulated during cell development and stress response. In order to detect actively translated open reading frame (ORF) and dynamic cellular translation events, we have developed a computational method, RiboWave, to process ribosome profiling data. RiboWave utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes and precisely locate their footprint denoted as Periodic Footprint P-site (PF P-site). Such high-resolution footprint is found to capture the full track of actively elongating ribosomes, from which translational landscape can be explicitly characterized. Original-Maintainer: Zhiyu Xu Package: rna-star Version: 2.7.11b-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: zlib1g-dev Filename: ./rna-star_2.7.11b-0lbi_amd64.deb Size: 1511968 MD5sum: 5c6be567f0efbf1761333fd7063a2374 SHA1: 40aab6e099568338850402d4eecb91fab5cac523 SHA256: fa9f927872108b9d2294d21fb268b13f2a45263f8ffdc8127e2500390f5d95a1 Section: science Priority: optional Homepage: https://github.com/alexdobin/STAR Description: Spliced Transcripts Alignment to a Reference Original-Maintainer: Alex Dobin Package: rseqc Version: 3.0.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: cython3 (>= 0.17), python3 (>= 3.5), python3-bx, python3-numpy, python3-pybigwig, python3-pysam Filename: ./rseqc_3.0.0-0lbi_all.deb Size: 86816 MD5sum: 167868acf1719b4efe1ebee78a1eaf80 SHA1: 9a97c608133df9ac591c4fb8eb4f2240dc9805a3 SHA256: e0b666992f9dc61b3884fedf5dafdcf6d7f195de677ab788990f70ef32c65987 Section: science Priority: optional Homepage: http://rseqc.sourceforge.net/ Description: Comprehensive QC package for RNA-seq data RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. Original-Maintainer: Liguo Wang Package: rstudio-server Version: 1.4.1717 Architecture: amd64 Maintainer: RStudio Installed-Size: 569315 Depends: psmisc, libapparmor1, libedit2, sudo, lsb-release, libssl1.0.0 | libssl1.0.2 | libssl1.1, libclang-dev, libsqlite3-0, libpq5, libc6 (>= 2.7) Recommends: r-base (>= 3.0.1) Filename: ./third-party/rstudio-server-1.4.1717-amd64.deb Size: 57613138 MD5sum: 7a125b0715ee38e00e5732fd3306ce15 SHA1: 413bcc57fe0c555c3a22b2d5dae469a4d5330a2d SHA256: ce2c6d5423823716bbd6c2d819812ed98b6ab3ea96bcfdbc6d310fd1c1286b17 Section: devel Priority: optional Description: RStudio Server RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management. Package: rstudio-server Version: 2022.02.2+485 Architecture: amd64 Maintainer: RStudio Installed-Size: 311803 Depends: psmisc, libapparmor1, libedit2, sudo, lsb-release, libssl1.0.0 | libssl1.0.2 | libssl1.1, libclang-dev, libsqlite3-0, libpq5, libc6 (>= 2.7) Recommends: r-base (>= 3.0.1) Filename: ./third-party/rstudio-server-2022.02.2-485-amd64.deb Size: 62884858 MD5sum: 0fb9fe6002d4808834cfbdaed3364b29 SHA1: aa44ce7eca24e27430d12c3346a040390fddf7bb SHA256: d339220473477b8740aada8f41017ed2094c665e94bc63b43d1a511f448ecbdb Section: devel Priority: optional Description: RStudio Server RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management. Package: rstudio-server Version: 2023.12.1+402 Architecture: amd64 Maintainer: RStudio Installed-Size: 594160 Depends: libssl-dev, psmisc, libclang-dev, libsqlite3-0, lsb-release, sudo, libc6 (>= 2.7) Suggests: r-base (>= 3.3.0) Filename: ./third-party/rstudio-server-2023.12.1-402-amd64.deb Size: 105258320 MD5sum: 62bf4d7653bfa5f97079ae7e7e1d1705 SHA1: edecaa94cb4e371a83d894be8cc86392bd5f6c4a SHA256: 2ceeebe5d1d77068b36e85f7cf366cd1409f7642a80261b6bbeb3da945ef0888 Section: devel Priority: optional Description: RStudio Server RStudio is an integrated development environment (IDE) designed to support multiple languages, including both R and Python. It includes a console, syntax-highlighting editor that supports direct code execution, and a variety of robust tools for plotting, viewing history, debugging and managing your workspace. Package: sailfish Version: 0.10.0-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./sailfish_0.10.0-1lbi_amd64.deb Size: 2873564 MD5sum: ab1feeffd389dc052976a061940e3e2c SHA1: 5a13a4db18b70630424c8a58bc157101508752e5 SHA256: 80c1b94267ef95f1e42b32a946d0ffeeaf6abad0d0c47d019be5935ee3f7291e Section: science Priority: optional Homepage: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Description: Rapid Alignment-free Quantification of Isoform Abundance Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads. Rather than working at the read level, the fundamental unit of transcript coverage in Sailfish is the k-mer. Implementing this alternative, lightweight, approach allows Sailfish to dispense with many of the complexities of read mapping while remaining robust to sequencing errors. By replacing read mapping with intelligent k-mer indexing and counting, Sailfish is able to quantify isoform abundance orders of magnitude faster than existing tools. Original-Maintainer: Rob Patro Package: salmon Version: 1.10.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: ca-certificates, curl, libboost-all-dev, libbz2-dev, liblzma-dev, unzip, zlib1g-dev Filename: ./salmon_1.10.0-0lbi_amd64.deb Size: 62355910 MD5sum: 93dbfffae54fe8f6032363e759d4a7cc SHA1: 67c9c2ff41092ade4244720cebd03742adfdd30a SHA256: 8030ffa83b2873ddb8ee8795d4efe12d7423ae42dd771770e5f34c6eb60dc430 Section: science Priority: optional Homepage: https://github.com/COMBINE-lab/salmon Description: Transcript-level quantification from RNA-seq reads Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective- alignment (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many different pipelines. For example, you can choose to make use of our selective-alignment algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file with alignments to the transcriptome produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. Original-Maintainer: Rob Patro , Salmon Package: sat-assembler Version: 2016-01-20-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: hmmer (>= 3.0), python2 (>= 2.5), python-biopython, python-networkx Filename: ./sat-assembler_2016-01-20-1lbi_amd64.deb Size: 246648 MD5sum: cebf15fd2cbd6e13c1c1d7c4b87a7497 SHA1: 00b1d95d33c12436a82f16fb35b1d10be8dfd2b3 SHA256: af6e9d6022d878cb11005d782c57ea2773a79f72a954e875851378cf96137f77 Section: science Priority: optional Homepage: https://sourceforge.net/projects/sat-assembler/ Description: Scalable and accurate targeted gene assembly for large-scale NGS data SAT-Assembler is a scalable and accurate gene assembly tool for large-scale RNA-Seq and metagenomic data. It recovers genes from gene families of particular interest to biologists with high coverage, low chimera rate, and extremely low memory usage compared with exiting gene assembly tools. Moreover, it is naturally compatible with parallel computing platforms. Original-Maintainer: Yuan Zhang , Yanni Sun Package: scallop Version: 0.10.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: coinor-libclp-dev, libboost-dev, libhts-dev Filename: ./scallop_0.10.2-0lbi_amd64.deb Size: 3868444 MD5sum: 772f0cebfe1285ee52a15a5b5161799a SHA1: 7eacab8919eb32a9165a9e493e3546c445d0dd76 SHA256: 1a17a3c7de7874d7960fa651e3a82e5e742c0887c99f15b7d9132c0ad52633c6 Section: science Priority: optional Homepage: https://github.com/Kingsford-Group/scallop Description: Scallop is a reference-based transcriptome assembler for RNA-seq Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviation minimization. Original-Maintainer: Mingfu Shao Package: screamingbackpack Version: 0.2.333-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./screamingbackpack_0.2.333-0lbi_amd64.deb Size: 23478 MD5sum: dbad52dc32d04cc99de7544a30512bcb SHA1: 1f69b6646a4a4b548816c19ee20248ca652246cd SHA256: 7b67d485314c5582dec91aba0e67c902d2b0a1a2c040d55d3a821e0162b9066e Section: science Priority: optional Homepage: http://pypi.python.org/pypi/ScreamingBackpack/ Description: Handing syncing of remote and local data resources The utility works by placing a small file (manifest file) in the data directory that describes the file names, their locations and if possible their hashes (sha256). This file is downloaded during diff and update functions and is used to determine what other file operations (downloads / deletions) should occur. Original-Maintainer: Michael Imelfort Package: seecer Version: 0.1.3-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: jellyfish, libgsl-dev| libgsl0-dev, libopenmpi-dev, seqan-apps Filename: ./seecer_0.1.3-1lbi_amd64.deb Size: 912348 MD5sum: d434000924468bed92c95ebdd3a26d92 SHA1: 383b2fbbbf91b71512c0621e057bdd5f0797de90 SHA256: 92e0fb022f075c2449e9f5174bc1feb7b6f3490c6d348663ab95cf1035620465 Section: science Priority: optional Homepage: http://sb.cs.cmu.edu/seecer/ Description: SEquencing Error CorrEction for Rna reads SEECER is a sequencing error correction algorithm for RNA-seq data sets. It takes the raw read sequences produced by a next generation sequencing platform like machines from Illumina or Roche. SEECER removes mismatch and indel errors from the raw reads and significantly improves downstream analysis of the data. Especially if the RNA-Seq data is used to produce a de novo transcriptome assembly, running SEECER can have tremendous impact on the quality of the assembly. Original-Maintainer: Hai-Son Le , Marcel Schulz , Ziv Bar-Joseph Package: seg Version: 1994.18.10-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./seg_1994.18.10-0lbi_amd64.deb Size: 76284 MD5sum: 9eba9f1c0893073d2468287a0f15e054 SHA1: ffd59f4233db9a457baebd875a6cc5303c795423 SHA256: c746f5392fe2195681380add91dfc98da0973e2f8619b50d0b974a7f0770a670 Section: science Priority: optional Homepage: ftp://ftp.ncbi.nih.gov/pub/seg/seg/ Description: seg - segment sequence(s) by local complexity This package contains the SEG program of Wootton and Federhen, for identifying and masking segments of low compositional complexity in amino acid sequences. This program is inappropriate for masking nucleotide sequences and, in fact, may strip some nucleotide ambiguity codes from nt. sequences as they are being read. Original-Maintainer: John Wootton , Scott Federhen Package: sepp Version: 4.5.1-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: default-jre, hmmer, pplacer, python3-dendropy (>= 4.0.0) Filename: ./sepp_4.5.1-0lbi_all.deb Size: 1623112 MD5sum: 79cf51a6c98baec00397577e974f122a SHA1: 5daad71d8ddc1559e6833c21401813aef2c9a928 SHA256: 1bcd5c6b1441179f593e5172b91204002ede36fdf272a7095e80c47e611f9e1d Section: science Priority: optional Homepage: https://github.com/smirarab/sepp Description: SATe enabled phylogenetic placement This package SEPP, TIPP, UPP, HIPPI. Each method uses ensembles of Hidden Markov Models (HMMs) in a different way, each focusing on a different problem. Original-Maintainer: Siavash Mirarab , Nam Nguyen Package: seq-crumbs Version: 0.1.9-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-biopython (>= 1.60), python-bz2file Filename: ./seq-crumbs_0.1.9-1lbi_amd64.deb Size: 1096916 MD5sum: a8ee889b1a86266495cbd68611de66f7 SHA1: fa1ff82f87c34f9a2b77d516b96fb6b92f26f72a SHA256: 77663b009659aa04ff1b0e1abb616986c8402368b537e4dc9fab4d7ef813fe12 Section: science Priority: optional Homepage: http://bioinf.comav.upv.es/seq_crumbs/ Description: Small utilities for sequence files manipulation seq_crumbs is modeled after the Unix command line text processing utilities so every utility tries to perform a specific task and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utilities with Unix pipes to create complex pipelines. There are already other similar software that uses this approach like fastx and biopieces. Original-Maintainer: Jose Blanca Package: seqkit Version: 0.10.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./seqkit_0.10.1-0lbi_amd64.deb Size: 2527660 MD5sum: 111fc9410c9624cc18ef972666eabdaa SHA1: ed9e88a5a3ff7bce5a7b19e29621a3627b10df48 SHA256: c24ef3b56fdacf948f9a1b9fe750c5c41082f24c6f993824bbac837c63176d8a Section: science Priority: optional Homepage: https://bioinf.shenwei.me/seqkit/ Description: An ultrafast toolkit for FASTA/Q file manipulation FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. . SeqKit is an ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. Original-Maintainer: Wei Shen Package: sequin Version: 15.10-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./sequin_15.10-0lbi_amd64.deb Size: 6596014 MD5sum: 8b991445e1d3fe17c4419227224fe5ea SHA1: c1d2ef123a8700519ece02e34b8e775ba530ff77 SHA256: c618f904d8268ca5e6890de2008f77c7165569396ee4c8c04f2cfeef18d1c210 Section: science Priority: optional Homepage: http://www.ncbi.nlm.nih.gov/projects/Sequin/ Description: A DNA Sequence Submission and Update Tool Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, gapped sequences, or phylogenetic and population studies. A single Sequin file should contain less than 10,000 sequences for maximum performance. Larger submissions should be made with tbl2asn. Original-Maintainer: NCBI Service Desk Package: sff2fastq Version: 0.9.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./sff2fastq_0.9.2-0lbi_amd64.deb Size: 11344 MD5sum: af017a38e582769e35e46861913f397a SHA1: b41b0eaf0f814d6346f55aa4f9de7008b6120d77 SHA256: 0623599a4bb66b818d847d139664fa2b70e9ab628b25182f1daaf8cde643b6e0 Section: science Priority: optional Homepage: https://github.com/indraniel/sff2fastq Description: Convert 454 Genome Sequencer reads from a SFF file to FASTQ The program `sff2fastq` extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format. Original-Maintainer: Indraniel Das Package: shortbred Version: 0.9.5-3lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: cd-hit (>= 4.6), muscle (>= 3.8.31), ncbi-blast+ (>= 2.2.28), python2 (>= 2.7), python-biopython (>= 1.63) Filename: ./shortbred_0.9.5-3lbi_all.deb Size: 32408 MD5sum: 9bd2030d0029ffb6ef7a38fb0838a777 SHA1: 4e6a7a7994028c922da62efc5dbff14ad98689bc SHA256: 2d2ef1028b65d333a4fe309e542422e06cea03ab343e48ab123a431920d8b5d5 Section: science Priority: optional Homepage: https://huttenhower.sph.harvard.edu/shortbred Description: Short, Better Representative Extract Dataset ShortBRED is a pipeline to take a set of protein sequences, group them into families, extract a set of distinctive strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest. Original-Maintainer: Jim Kaminski Package: shrimp Version: 2.2.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: openmpi-bin Filename: ./shrimp_2.2.3-0lbi_amd64.deb Size: 893978 MD5sum: fee14d25c739e55d300aad47fa53b5bc SHA1: 9b7cc12f856a890c0d196b40a0721e6e44a2fe5d SHA256: 6ea3c7d241721eced42e66d39586e43379caeba0cf7f1fb3db9200528134f05e Section: science Priority: optional Homepage: http://compbio.cs.toronto.edu/shrimp/ Description: SHRiMP - SHort Read Mapping Package SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation. Original-Maintainer: Michael Brudno Package: sicer2 Version: 1.0.3-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3, python3-numpy, python3-scipy (>= 1.0.0) Filename: ./sicer2_1.0.3-0lbi_amd64.deb Size: 384960 MD5sum: 034be37cf18f1ce103df863783953fc1 SHA1: 23fe9dda894f3684b69f14c355c7b7b118adc5c8 SHA256: 72ba542a18854858d3cb1c1f23f3950b5c388816161d39a04484ebfa68132e87 Section: science Priority: optional Homepage: http://zanglab.github.io/SICER2 Description: Redesigned and improved ChIP-seq broad peak calling tool Redesigned and improved version of the original ChIP-seq broad peak calling tool SICER. Also contains Coarse-graining Approach for Identifying Broad Domains from ChIP-Enriched Regions (RECOGNICER) Original-Maintainer: Chongzhi Zang Package: singularity-ce Version: 3.9.1+6-g38b50cbc5-focal Architecture: amd64 Maintainer: Sylabs Community Packaging Installed-Size: 126075 Depends: libc6 (>= 2.14), libseccomp2 (>= 2.4.1), cryptsetup-bin, squashfs-tools Conflicts: singularity-container, singularitypro24, singularitypro25, singularitypro26, singularitypro31, singularitypro35, singularitypro37, singularitypro39 Filename: ./third-party/singularity-ce_3.9.1+6-g38b50cbc5-focal_amd64.deb Size: 27139812 MD5sum: efbf0254d016677a7310fd965209dab6 SHA1: 908d11777a6d49d93771b850fdca7c6fd10679f9 SHA256: b9193cf439bcd9a21e995dfb064eb6155c851a4bf4bc93210a94c83fee1d0bd0 Section: admin Priority: optional Homepage: https://sylabs.io/singularity Description: SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure. Package: solar-eclipse Version: 8.5.1-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: gzip Filename: ./solar-eclipse_8.5.1-1lbi_amd64.deb Size: 7577276 MD5sum: 61e3b968a31d73235889255a0d57d127 SHA1: 522141dd0886ed8a45524fee3ce9f1bf1dba7bb5 SHA256: 9ad96bc6346d117d1ee833b37831808e5055dda8a2f7a19f21d9f1c1fe92e36d Section: science Priority: optional Homepage: http://solar-eclipse-genetics.org/ Description: An Imaging Genetics Analyses Software SOLAR-Eclipse is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of multiple quantitative traits and/or discrete traits which may involve multiple loci (oligogenic analysis), dominance effects, household effects, and interactions. Additional features include functionality for mega and meta-genetic analyses where data from diverse cohorts can be pooled to improve statistical significance. Original-Maintainer: Solar-Eclipse Team Package: spades Version: 4.0.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3 (>= 3.8) Filename: ./spades_4.0.0-0lbi_amd64.deb Size: 137991596 MD5sum: db498deb25c56ff3a606bf221739c4ad SHA1: bff2e3fe58a1b315533c366dd8797b4c42bd5d98 SHA256: 919e8ad13734204064ba5d7d72cc529add89dad1a83f3ef3ef327d8b2844e083 Section: science Priority: optional Homepage: http://cab.spbu.ru/software/spades/ Description: SPAdes Genome Assembler SPAdes is a versatile toolkit designed for assembly and analysis of sequencing data. SPAdes is primarily developed for Illumina sequencing data, but can be used for IonTorrent as well. Most of SPAdes pipelines support hybrid mode, i.e. allow using long reads (PacBio and Oxford Nanopore) as a supplementary data. . SPAdes package contains assembly pipelines for isolated and single-cell bacterial, as well as metagenomic and transcriptomic data. Additional modes allow to discover bacterial plasmids and RNA viruses, as well as perform HMM-guided assembly. Besides, SPAdes package includes supplementary tools for efficient k-mer counting and k-mer-based read filtering, assembly graph construction and simplification, sequence-to-graph alignment and metagenomic binning refinement. Original-Maintainer: Spades Support Package: spingo Version: 1.3-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python2 (>= 2.7), python2 (<< 3) Filename: ./spingo_1.3-1lbi_amd64.deb Size: 659072 MD5sum: 2670de37041635f6b8c4ebf98c167d95 SHA1: 4ef6a87c60c2cd3cead5722b2c73062f4352b44a SHA256: 9800fe2fa955ad55dd204694bc44550cc3de79aa465eb7c955392c8bdb3f9385 Section: science Priority: optional Homepage: https://github.com/GuyAllard/SPINGO Description: SPecies level IdentificatioN of metaGenOmic amplicons SPINGO - SPecies level IdentificatioN of metaGenOmic amplicons (alternatively: an olde English word meaning ‘strong beer’) Original-Maintainer: Marcus Claesson Package: spladder Version: 1.1.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python-h5py (>= 2.2.0), python-intervaltree, python-matplotlib (>= 1.4.0), python-pysam (>= 0.7), python-scipy (>= 0.12) Filename: ./spladder_1.1.0-0lbi_amd64.deb Size: 146374 MD5sum: ddc3e44d6a84ab3be2b818387a0a3fd9 SHA1: 54165e4cd1bb3390fce6d1e5155e0d8dcf92fe40 SHA256: f13f8d51e2c0a958304fa9dc31ef07855b36458db4baa6fb5275d59c3a9121f9 Section: science Priority: optional Homepage: https://github.com/ratschlab/spladder Description: Detection and quantification of alternative splicing events SplAdder, short for Splicing Adder, is a toolbox for alternative splicing analysis based on RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events based on the alignment data. The quantified events can then be used for differential analysis. Original-Maintainer: Andre Kahles Package: splign Version: 2.0.8-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libpcre3 Filename: ./splign_2.0.8-0lbi_amd64.deb Size: 9371146 MD5sum: 2b2d439344c1f706572a37f18432336b SHA1: 98b30704ffa63e5c32e0f928ad1d8f5b83a80bf6 SHA256: 51c607bbca7309fd861656e12392c9634c69c0db5bf8e857b1c230426d079a00 Section: science Priority: optional Homepage: http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi Description: Computes spliced sequence alignments Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a compartmentization algorithm which identifies possible gene duplications, and a refined alignment algorithm recognizing introns and splice signals. Original-Maintainer: Yuri Kapustin Package: sra-toolkit Version: 3.3.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: libmagic1 (>= 5.12), libxml2 Filename: ./sra-toolkit_3.3.0-0lbi_amd64.deb Size: 22614014 MD5sum: 87a192772e8765142f2e90f265919730 SHA1: 473bf394d9bf95284bcb063a7d15eb1f47e678dd SHA256: f913ff6a1f1ccc9a371444bfe774794254082c55d528b62f37f04c01edb4e901 Section: science Priority: optional Homepage: https://github.com/ncbi/sra-tools/ Description: NCBI Sequence Read Archive Tools The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Original-Maintainer: SRA Package: stringtie Version: 1.3.4d-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: samtools Recommends: cufflinks Filename: ./stringtie_1.3.4d-0lbi_amd64.deb Size: 1117408 MD5sum: a729dec7d782fb2a4977ded74e9d169b SHA1: 9f9dc8888a6a17fa86f5ebdcc93f3a6e393f878e SHA256: 440e418f889f3fc967db70a61a96f08e7151124bcd242530ba815428348fb499 Section: science Priority: optional Homepage: http://ccb.jhu.edu/software/stringtie/ Description: Transcript assembly and quantification for RNA-Seq StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads. To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs. Original-Maintainer: Mihaela Pertea Package: suppa Version: 2.3-1lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: python3, python3-statsmodels Filename: ./suppa_2.3-1lbi_amd64.deb Size: 73052 MD5sum: cb804606e753a99d9c11d81ee0d935de SHA1: 85a711e449609a210971d7d542c0ab623d1ac088 SHA256: 409b609d472278e334435ac288a276cb1a29d2f9021c2905afdec9285f74861f Section: science Priority: optional Homepage: https://github.com/comprna/SUPPA Description: Fast quantification of differential splicing SUPPA is a flexible and powerful tool to study splicing at the transcript isoform or at the local alternative splicing event level, across multiple conditions, and at high speed and accuracy. Original-Maintainer: Gael P Alamancos , Eduardo Eyras Package: taxonkit Version: 0.3.0-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./taxonkit_0.3.0-0lbi_amd64.deb Size: 2090768 MD5sum: fdc1df5962ae7af1f132165e508ec821 SHA1: e6deaaf0bc4d8235fe023545280456187caf6bc1 SHA256: f450a0e2290075e565a2cc1e95a658f0e33c56d1a60e7812e391c0777d9fd950 Section: science Priority: optional Homepage: https://bioinf.shenwei.me/taxonkit/ Description: Efficient NCBI Taxonomy Toolkit TaxonKit - A cross-platform and Efficient NCBI Taxonomy Toolkit Original-Maintainer: Wei Shen Package: tbl2asn Version: 25.8-2lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./tbl2asn_25.8-2lbi_amd64.deb Size: 3963000 MD5sum: 6815dba694305de1d28a0176c0443cfb SHA1: 424b293be4a51f90fb9c1522d7f676f60b5519b8 SHA256: cec2320d2f4eb3fc6bf9802d70709ce679bb0be5ab0e116212f994aa3d23542b Section: science Priority: optional Homepage: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ Description: Short description. Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before submission. Original-Maintainer: NCBI Tools Package: tophat Version: 2.1.1+lbi-1 Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: bowtie2 | bowtie, libc6 (>= 2.15), libstdc++6 (>= 5.2), python2, zlib1g Suggests: cufflinks Filename: ./tophat_2.1.1+lbi-1_amd64.deb Size: 6418708 MD5sum: f82e685ff582a6967a619a70b9856422 SHA1: d8ee0a5144f0e0ec6a68f0fb28ba3badea97d61f SHA256: 285c694dd67f3dbcdd9041b70609ee62d3914133a2dd4ef51aaa7133d187a5a6 Section: science Priority: optional Homepage: http://ccb.jhu.edu/software/tophat Description: fast splice junction mapper for RNA-Seq reads TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology. Original-Maintainer: TopHat Authors Package: trim-galore Version: 0.5.0-0lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: cutadapt, fastqc, perl Filename: ./trim-galore_0.5.0-0lbi_all.deb Size: 736040 MD5sum: 9ac0a528411d3d1ea5b207b2871fe7d5 SHA1: 587ff18dde015cebaf1bbd0ea3d2a86e7ccbd444 SHA256: b92629e7f68e60573aac290d4c2815a32c12e2cb2ec4ab407781a459e83f12e1 Section: science Priority: optional Homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Description: Quality and adapter trimming for RRBS or standard FastQ files Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. Original-Maintainer: Felix Krueger Package: trimal Version: 1.4.1-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Filename: ./trimal_1.4.1-0lbi_amd64.deb Size: 144224 MD5sum: e44b451e424d199c428af7cc1fbb2962 SHA1: 6cee070a51ca4095ed6c41c725197da614f72db5 SHA256: f1bda52a31841d9044eaec097431dace37a5006fdc6c3438c04f4ddd9b272806 Section: science Priority: optional Homepage: http://trimal.cgenomics.org/trimal Description: A tool for automated alignment trimming trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. . trimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, the consistency level of columns among alignments. Moreover, trimAl is able to manually select a set of columns to be removed from the alignment. Original-Maintainer: Salvador Capella-Gutierrezv , Toni Gabaldón Package: trinityrnaseq Version: 2.15.2-0lbi Architecture: amd64 Maintainer: Laboratório de Bioinformática Depends: berkeley-express, bowtie2, jellyfish, libgetopt-java, libjung-free-java, openjdk-8-jre, parafly, r-bioc-qvalue, salmon Recommends: trinityrnaseq-examples Filename: ./trinityrnaseq_2.15.2-0lbi_amd64.deb Size: 36540724 MD5sum: 569fc247ad0fb76d057e308e01c5e4db SHA1: 9653786c652eca627b4674232e251b615b96576f SHA256: c607ef8548e82e219536af7d1445fdb705e61b6c5ce2c4ae89831e60ad26c3d9 Section: science Priority: optional Homepage: http://trinityrnaseq.github.io/ Description: RNA-Seq De novo Assembly Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. . Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. . Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Original-Maintainer: Trinity user list Package: tv Version: 0.5.3 Architecture: amd64 Maintainer: codechenx Installed-Size: 4860 Filename: ./third-party/tv_0.5.3_linux_amd64.deb Size: 1929250 MD5sum: c7dd11a12b4679f1b4ceabc770b6a07d SHA1: 83c3468d77c3c7a3dd9451e4494a51364678c29f SHA256: 04bd143162f35fe0c88c067158f0175fe7edacafd40a2bb819d47e11afe1ba62 Homepage: https://github.com/codechenx/tv Description: tv is a tool to view the delimited file in terminal. Package: wgs-tools Version: 0-1lbi Architecture: all Maintainer: Laboratório de Bioinformática Depends: sra-toolkit Filename: ./wgs-tools_0-1lbi_all.deb Size: 4282 MD5sum: 8875be59f791925f0ac5a0b257648605 SHA1: 4ec200ef43a69464f0fe14b1aa654201111d212a SHA256: 7e59e277814d61f6b677025dc3cccd23ea3043e5b449b2cd2717524535394581 Section: science Priority: optional Homepage: ftp://ftp.ncbi.nlm.nih.gov/blast/WGS_TOOLS/ Description: Stand-alone BLAST and WGS projects The National Center for Biotechnology Information (NCBI) is introducing a new way to search Whole Genome Shotgun (WGS) projects with stand-alone BLAST. The explosive growth of the WGS sequences means it is no longer feasible to search all WGS projects, but rather it is necessary to search a taxonomic subset of WGS. To allow this, the NCBI is providing BLAST executables called blastn_vdb and tblastn_vdb. These executables perform the same tasks as blastn and tblastn, except they can search the WGS archives directly. See the README file for details. Original-Maintainer: BLAST Help