recipe bioconductor-gispa

GISPA: Method for Gene Integrated Set Profile Analysis






GISPA is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile. GISPA method has been previously published in Nucleic Acid Research (Kowalski et al., 2016; PMID: 26826710).

package bioconductor-gispa

(downloads) docker_bioconductor-gispa



depends bioconductor-biobase:


depends bioconductor-genefilter:


depends bioconductor-gseabase:


depends r-base:


depends r-changepoint:

depends r-data.table:

depends r-hh:

depends r-lattice:

depends r-latticeextra:

depends r-plyr:

depends r-scatterplot3d:



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-gispa

and update with::

   mamba update bioconductor-gispa

To create a new environment, run:

mamba create --name myenvname bioconductor-gispa

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-gispa/tags`_ for valid values for ``<tag>``)

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