recipe bioconductor-oppar

Outlier profile and pathway analysis in R







biotools: oppar

The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.

package bioconductor-oppar

(downloads) docker_bioconductor-oppar



depends bioconductor-biobase:


depends bioconductor-gseabase:


depends bioconductor-gsva:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends r-base:




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-oppar

and update with::

   mamba update bioconductor-oppar

To create a new environment, run:

mamba create --name myenvname bioconductor-oppar

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

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