- recipe rsem
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
- Homepage
- License
GPL3
- Recipe
- Links
doi: 10.1186/1471-2105-12-323, biotools: rsem
"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."
- package rsem¶
-
- Versions
1.3.3-4
,1.3.3-3
,1.3.3-2
,1.3.3-1
,1.3.3-0
,1.3.2-1
,1.3.2-0
,1.3.1-1
,1.3.1-0
,1.3.3-4
,1.3.3-3
,1.3.3-2
,1.3.3-1
,1.3.3-0
,1.3.2-1
,1.3.2-0
,1.3.1-1
,1.3.1-0
,1.3.0-4
,1.3.0-3
,1.3.0-2
,1.3.0-1
,1.3.0-0
,1.2.28-2
,1.2.28-0
,1.2.22-0
,1.2.21-5
,1.2.21-4
,1.2.21-3
- Depends
htslib
>=1.14,<1.15.0a0
libgcc-ng
>=10.3.0
libstdcxx-ng
>=10.3.0
perl
>=5.32.1,<5.33.0a0 *_perl5
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install rsem
and update with:
conda update rsem
or use the docker container:
docker pull quay.io/biocontainers/rsem:<tag>
(see rsem/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/rsem/README.html)