Package Recipe 'bioconductor-gsva'

recipe bioconductor-gsva

Gene Set Variation Analysis for Microarray and RNA-Seq Data

Homepage:: https://bioconductor.org/packages/3.20/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:

2.4.4-0, 2.0.0-1, 2.0.0-0, 1.50.0-1, 1.50.0-0, 1.48.2-0, 1.46.0-1, 1.46.0-0, 1.42.0-2,

2.4.4-0, 2.0.0-1, 2.0.0-0, 1.50.0-1, 1.50.0-0, 1.48.2-0, 1.46.0-1, 1.46.0-0, 1.42.0-2, 1.42.0-1, 1.42.0-0, 1.40.0-0, 1.38.2-0, 1.38.0-0, 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:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biobase >=2.70.0,<2.71.0a0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-biocsingular >=1.26.0,<1.27.0
on bioconductor-biocsingular >=1.26.1,<1.27.0a0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-delayedarray >=0.36.0,<0.37.0a0
on bioconductor-gseabase >=1.72.0,<1.73.0
on bioconductor-gseabase >=1.72.0,<1.73.0a0
on bioconductor-hdf5array >=1.38.0,<1.39.0
on bioconductor-hdf5array >=1.38.0,<1.39.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0a0
on bioconductor-s4arrays >=1.10.0,<1.11.0
on bioconductor-s4arrays >=1.10.1,<1.11.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0
on bioconductor-sparsearray >=1.10.0,<1.11.0
on bioconductor-sparsearray >=1.10.8,<1.11.0a0
on bioconductor-sparsematrixstats >=1.22.0,<1.23.0
on bioconductor-sparsematrixstats >=1.22.0,<1.23.0a0
on bioconductor-spatialexperiment >=1.20.0,<1.21.0
on bioconductor-spatialexperiment >=1.20.0,<1.21.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-cli
on r-matrix >=1.5-0
on r-memuse

Additional platforms:

linux-aarch64

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 bioconductor-gsva

to add into an existing workspace instead, run:

pixi add bioconductor-gsva

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 bioconductor-gsva

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gsva

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/bioconductor-gsva:<tag>

(see bioconductor-gsva/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.

Download stats¶

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)