cosmosR

DOI: 10.18129/B9.bioc.cosmosR    

COSMOS (Causal Oriented Search of Multi-Omic Space)

Bioconductor version: Release (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 uni-heidelberg.de>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cosmosR")

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

Documentation

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

browseVignettes("cosmosR")

 

HTML R Script cosmosR tutorial
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics
Version 1.0.0
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, org.Hs.eg.db, visNetwork
LinkingTo
Suggests testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL https://github.com/saezlab/COSMOSR
BugReports https://github.com/saezlab/COSMOSR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package cosmosR_1.0.0.tar.gz
Windows Binary cosmosR_1.0.0.zip
macOS 10.13 (High Sierra) cosmosR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cosmosR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cosmosR
Package Short Url https://bioconductor.org/packages/cosmosR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive

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