recipe bioconductor-cmapr

CMap Tools in R






The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets.

package bioconductor-cmapr

(downloads) docker_bioconductor-cmapr



depends bioconductor-flowcore:


depends bioconductor-rhdf5:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-data.table:

depends r-matrixstats:



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-cmapr

and update with::

   mamba update bioconductor-cmapr

To create a new environment, run:

mamba create --name myenvname bioconductor-cmapr

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

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