recipe bioconductor-cosmosr

COSMOS (Causal Oriented Search of Multi-Omic Space)






COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.

package bioconductor-cosmosr

(downloads) docker_bioconductor-cosmosr



depends bioconductor-carnival:


depends bioconductor-decoupler:


depends bioconductor-dorothea:


depends bioconductor-gseabase:


depends r-base:


depends r-dplyr:

depends r-igraph:

depends r-progress:

depends r-purrr:

depends r-rlang:

depends r-stringr:

depends r-visnetwork:



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-cosmosr

and update with::

   mamba update bioconductor-cosmosr

To create a new environment, run:

mamba create --name myenvname bioconductor-cosmosr

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

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