DOI: 10.18129/B9.bioc.cosmosR    

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 (3.15)

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 <dugourdaurelien at>, Attila Gabor <attila.gabor at>, Katharina Zirngibl <katharina.zirngibl at>

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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License GPL-3
Depends R (>= 4.1)
Imports AnnotationDbi, biomaRt, CARNIVAL, dorothea, dplyr, ggplot2, GSEABase, igraph, magrittr,, plyr, purrr, readr, rlang, scales, stringr, tibble, utils, visNetwork
Suggests testthat, knitr, rmarkdown, piano
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