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

Installers

Info: This package contains files in non-standard labels.

conda install

  • linux-64  v1.3.3
  • osx-64  v1.3.3
To install this package with conda run one of the following:
conda install -c bioconda rsem
conda install -c bioconda/label/cf201901 rsem

Description

"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."


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