recipe rsem

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

Homepage:

https://deweylab.github.io/RSEM

Developer docs:

https://github.com/deweylab/RSEM

License:

GPL3 / GPL-3.0-or-later

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

(downloads) docker_rsem

Versions:
1.3.3-12,  1.3.3-11,  1.3.3-10,  1.3.3-9,  1.3.3-7,  1.3.3-6,  1.3.3-5,  1.3.3-4,  1.3.3-3, 

1.3.3-12,  1.3.3-11,  1.3.3-10,  1.3.3-9,  1.3.3-7,  1.3.3-6,  1.3.3-5,  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:

  • on bioconductor-biobase

  • on bioconductor-ebseq

  • on htslib >=1.22.1,<1.23.0a0

  • on libgcc >=13

  • on libstdcxx >=13

  • on libzlib >=1.3.1,<2.0a0

  • on perl >=5.32.1,<5.33.0a0 *_perl5

  • on perl-module-build 0.4234.*

  • on r-base

  • on samtools

  • on ucsc-bigwigsummary

Additional platforms:
linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install rsem

to add into an existing workspace instead, run:

pixi add rsem

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install rsem

Alternatively, to install into a new environment, run:

conda create -n envname rsem

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/rsem:<tag>

(see rsem/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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