recipe bioconductor-gsva

Gene Set Variation Analysis for microarray and RNA-seq data

Homepage

https://bioconductor.org/packages/3.11/bioc/html/GSVA.html

License

GPL (>= 2)

Recipe

/bioconductor-gsva/meta.yaml

Links

biotools: gsva

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

package bioconductor-gsva

Versions

1.36.0-0, 1.34.0-0, 1.32.0-1, 1.30.0-1, 1.30.0-0, 1.28.0-0, 1.26.0-0, 1.24.2-0, 1.24.1-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-gseabase >=1.50.0,<1.51.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• r-base >=4.0,<4.1.0a0

• r-fastmatch

• r-shiny

• r-shinythemes

Required By

• bioconductor-consensusov

• bioconductor-tbsignatureprofiler

• r-xcell

• r-sigqc

• bioconductor-singlecelltk

• bioconductor-egsea

• bioconductor-oppar

• r-immunedeconv

• bioconductor-sispa

• bioconductor-tnbc.cms

Installation

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

conda install bioconductor-gsva

and update with:

conda update bioconductor-gsva

or use the docker container:

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

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