Registration Open for Bioc2024
Early registration discount pricing ends May 31!


This is the development version of cosmosR; for the stable release version, see cosmosR.

COSMOS (Causal Oriented Search of Multi-Omic Space)

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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 1.13.0
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
Bug Reports
See More
Suggests testthat, knitr, rmarkdown, piano, ggplot2
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cosmosR_1.13.0.tar.gz
Windows Binary
macOS Binary (x86_64) cosmosR_1.13.0.tgz
macOS Binary (arm64) cosmosR_1.13.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats