[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Bug#778578: ITP: rsem -- RNA-Seq by Expectation-Maximization

Package: wnpp
Severity: wishlist
Owner: Debian Med team <debian-med@lists.debian.org>
X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org

* Package name    : rsem
  Version         : 1.2.19
  Upstream Author : Bo Li <bli25 [at] berkeley [dot] edu>
* 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.

Reply to: