recipe bioconductor-connectivitymap

Functional connections between drugs, genes and diseases as revealed by common gene-expression changes






The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules.

package bioconductor-connectivitymap

(downloads) docker_bioconductor-connectivitymap



depends bioconductor-data-packages:


depends curl:

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-connectivitymap

and update with::

   mamba update bioconductor-connectivitymap

To create a new environment, run:

mamba create --name myenvname bioconductor-connectivitymap

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

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