recipe bioconductor-srgnet

SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data

Homepage

https://bioconductor.org/packages/3.12/bioc/html/SRGnet.html

License

GPL-2

Recipe

/bioconductor-srgnet/meta.yaml

We developed SRGnet to analyze synergistic regulatory mechanisms in transcriptome profiles that act to enhance the overall cell response to combination of mutations, drugs or environmental exposure. This package can be used to identify regulatory modules downstream of synergistic response genes, prioritize synergistic regulatory genes that may be potential intervention targets, and contextualize gene perturbation experiments.

package bioconductor-srgnet

Versions

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0

Depends

• bioconductor-ebcoexpress >=1.34.0,<1.35.0

• bioconductor-limma >=3.46.0,<3.47.0

• r-base >=4.0,<4.1.0a0

• r-dmwr >=0.4.1

• r-gbm >=2.1.1

• r-hmisc

• r-igraph

• r-mass

• r-matrixstats

• r-pvclust >=2.0-0

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-srgnet

and update with:

conda update bioconductor-srgnet

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-srgnet:<tag>

(see bioconductor-srgnet/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/bioconductor-srgnet/README.html)