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COSMOS (Causal Oriented Search of Multi-Omic Space)

Bioconductor version: Release (3.18)

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.

Author: Aurélien Dugourd [aut] , Attila Gabor [cre] , Katharina Zirngibl [aut]

Maintainer: Attila Gabor <attila.gabor at uni-heidelberg.de>

Citation (from within R, enter citation("cosmosR")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

cosmosR tutorial HTML R Script
Reference Manual PDF


biocViews CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.1)
Imports CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR
System Requirements
URL https://github.com/saezlab/COSMOSR
Bug Reports https://github.com/saezlab/COSMOSR/issues
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Suggests testthat, knitr, rmarkdown, piano, ggplot2
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cosmosR_1.10.0.tar.gz
Windows Binary cosmosR_1.10.0.zip
macOS Binary (x86_64) cosmosR_1.10.0.tgz
macOS Binary (arm64) cosmosR_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cosmosR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cosmosR
Bioc Package Browser https://code.bioconductor.org/browse/cosmosR/
Package Short Url https://bioconductor.org/packages/cosmosR/
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