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