recipe rsem

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

Homepage

https://deweylab.github.io/RSEM/

License

GPL3

Recipe

/rsem/meta.yaml

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

1.3.3-1,  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, 

1.3.3-1,  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

• bioconductor-biobase

• bioconductor-ebseq

• htslib >=1.10.2,<1.11.0a0

• libgcc-ng >=7.5.0

• libstdcxx-ng >=7.5.0

• perl >=5.26.2,<5.26.3.0a0

• perl-module-build

• r-base

• samtools

• ucsc-bigwigsummary

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>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/rsem/README.html)