recipe bioconductor-gsca

GSCA: Gene Set Context Analysis







biotools: gsca

GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.

package bioconductor-gsca

(downloads) docker_bioconductor-gsca



depends bioconductor-rhdf5:


depends r-base:


depends r-ggplot2:

depends r-gplots:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-shiny:

depends r-sp:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-gsca

and update with::

   mamba update bioconductor-gsca

To create a new environment, run:

mamba create --name myenvname bioconductor-gsca

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-gsca/tags`_ for valid values for ``<tag>``)

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