Bug#851468: ITP: python-galaxyxml -- XML Generation libraries for Galaxy Tool/ToolDeps XML
Package: wnpp Severity: wishlist Owner: anton.kho...@ukr.net * Package name: python-galaxyxml Version : 0.1 Upstream Author : Eric Rasche * URL : https://github.com/erasche/galaxyxml * License : Apache-2.0 Programming Lang: Python Description : XML Generation libraries for Galaxy Tool/ToolDeps XML Galaxy XML Generation Libraries support building of Tool XML and Tool Dependencies XML. The package is the dependency for argparse2tool. Remark: This package will be maintained bz the Debian Med team at https://anonscm.debian.org/git/debian-med/python-galaxyxml.git
Bug#778589: ITP: express -- Streaming quantification for high-throughput sequencing
Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: express Version : 1.5.1 Upstream Author : Adam Roberts & Lior Pachter * URL : http://bio.math.berkeley.edu/eXpress/index.html * License : Artistic-2.0 Programming Lang: C++ Description : Streaming quantification for high-throughput sequencing eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk. . In an analysis of the performance of eXpress for RNA-Seq data, we have observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias. . eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance. Express is a dependency of trinityrnaseq. The Debian Med team will be group maintaining it.
Bug#778587: ITP: r-cran-blockmodeling -- Generalized and classical blockmodeling of valued networks
Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: r-cran-blockmodeling Version : 0.1.8 Upstream Author : Ales Ziberna * URL : http://cran.fhcrc.org/web/packages/blockmodeling/index.html * License : GPL-2+ Programming Lang: R, Fortran Description : Generalized and classical blockmodeling of valued networks This R package is primarly meant as an implementation of Generalized blockmodeling for valued networks. In addition, measurese of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithem) can be computed and partitioned matrices can be ploted. r-cran-blockmodeling is a dependency of r-bioc-ebseq. It is group maintained by the Debian Med team.
Bug#778586: ITP: r-bioc-ebseq -- R package for RNA-Seq Differential Expression Analysis
Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: r-bioc-ebseq Version : 1.6.0 Upstream Author : Ning Leng * URL : https://www.biostat.wisc.edu/~kendzior/EBSEQ/ * License : Artistic-2.0 Programming Lang: R Description : R package for RNA-Seq Differential Expression Analysis r-bioc-ebseq is an R package for identifying genes and isoforms differentially expressed (DE) across two or more biological conditions in an RNA-seq experiment. EBSeq is an important program used in many bioinformatics pipelines. It is a dependency of the Trinity RNASeq assembler (trinityrnaseq). This package will be group maintained by the Debian Med team. ~
Bug#778578: ITP: rsem -- RNA-Seq by Expectation-Maximization
Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: rsem Version : 1.2.19 Upstream Author : Bo Li * URL : http://deweylab.biostat.wisc.edu/rsem/ * License : GPL-3 Programming Lang: C++, Perl Description : RNA-Seq by Expectation-Maximization RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute’s Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator. RSEM is a popular bioinformatics program and a dependency of trinityrnaseq. It will be maintained by the Debian Med team.
Bug#778489: ITP: jaligner -- implementation of the Smith-Waterman algorithm with Gotoh's improvement
Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: jaligner Version : 1.0 Upstream Author : Ahmed Moustafa * URL : http://jaligner.sf.net * License : GPL Programming Lang: Java Description : implementation of the Smith-Waterman algorithm with Gotoh's improvement JAligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model. jaligner is a dependency of many bioinformatic programs including trinityrnaseq. The packaging was started by Tim Booth and will be group maintained by the Debian Med team.
Bug#778331: ITP: parafly -- parallel command processing using OpenMP
Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: parafly Version : 0.0.2013.01.21 Upstream Author : Brian Haas * URL : http://parafly.sourceforge.net * License : BSD-3-clause Programming Lang: C++ Description : parallel command processing using OpenMP ParaFly provides a simple mechanism for running a predefined list of unix commands in parallel using multithreading. Failed processes are captured and reported. Successfully executed processes are noted. If the process is rerun, only those previously incompleted or failed processes will be executed. Parafly is a dependency of trinityrnaseq which is undergoing packaging. It is maintained by myself and the Debian Med team.
Bug#778300: ITP: transdecoder -- find coding regions within transcripts
Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: transdecoder Version : 2.0.1 Upstream Author : Brian Haas * URL : http://transdecoder.github.io/ * License : BSD-3-clause Programming Lang: Perl Description : find coding regions within transcripts TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. . TransDecoder identifies likely coding sequences based on the following criteria: . a minimum length open reading frame (ORF) is found in a transcript sequence . a log-likelihood score similar to what is computed by the GeneID software is > 0. . the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames. . if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc). . optional the putative peptide has a match to a Pfam domain above the noise cutoff score. transdecoder is a dependency of trinityrnaseq. It will be team maintained by myself and the Debian Med team.
Bug#778246: ITP: prokka -- rapid annotation of prokaryotic genomes
Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-devel@lists.debian.org, debian-...@lists.debian.org * Package name: prokka Version : 1.10 Upstream Author : Torsten Seemann * URL : http://www.vicbioinformatics.com/software.prokka.shtml * License : GPL-3+, CC0-1, CC-BY-ND-3 Programming Lang: Perl Description : rapid annotation of prokaryotic genomes A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. Prokka is a popular bioinformatics program. It will be team maintained by the Debian Med team.
Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
X-Debbugs-Cc: debian-...@lists.debian.org X-Debbugs-Cc: debian-devel@lists.debian.org Package: wnpp Severity: wishlist Owner: debian-...@lists.debian.org * Package name: bamtools Version : 2.2 Upstream Author : Derek Barnett * URL : https://github.com/pezmaster31/bamtools * License : Expat Programming Lang: C++ Description : C++ API and toolkit for manipulating BAM (genome alignment) files -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAD=wrcla-be-tyforwnmbje0nwwyahyli+7-nbdabnmmrau...@mail.gmail.com
