DOI: 10.18129/B9.bioc.cosmosR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see cosmosR.

COSMOS (Causal Oriented Search of Multi-Omic Space)

Bioconductor version: 3.13

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 [aut] , Katharina Zirngibl [cre, aut]

Maintainer: Katharina Zirngibl <katharina.zirngibl at>

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


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biocViews CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics
Version 1.0.1
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License GPL-3
Depends R (>= 4.1)
Imports CARNIVAL, dorothea, igraph, dplyr, utils, stringr, readr, rlang, tibble, purrr, AnnotationDbi, biomaRt,, visNetwork
Suggests testthat, knitr, rmarkdown
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