recipe r-consensustme

ConsensusTME is a consensus based approach to generating cancer specific gene sets for multiple cell types found within the tumour microenvironment. This package allows access to these genesets and provides a wrapper for using these gene sets with various statistical frameworks to generate normalised enrichment scores. These can be used to identify relative quantities of cell types across multiple samples.







doi: 10.1158/0008-5472.CAN-18-3560

package r-consensustme

(downloads) docker_r-consensustme


depends bioconductor-gseabase:

depends bioconductor-gsva:

depends bioconductor-singscore:

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 r-consensustme

and update with::

   mamba update r-consensustme

To create a new environment, run:

mamba create --name myenvname r-consensustme

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

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