cosmosR

DOI: 10.18129/B9.bioc.cosmosR    

COSMOS (Causal Oriented Search of Multi-Omic Space)

Bioconductor version: Release (3.14)

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>

Installation

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

if (!require("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	1.2.0
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
License	GPL-3
Depends	R (>= 4.1)
Imports	AnnotationDbi, biomaRt, CARNIVAL, dorothea, dplyr, ggplot2, GSEABase, igraph, magrittr, org.Hs.eg.db, plyr, purrr, readr, rlang, scales, stringr, tibble, utils, visNetwork
LinkingTo
Suggests	testthat, knitr, rmarkdown, piano
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_1.2.0.tar.gz
Windows Binary	cosmosR_1.2.0.zip
macOS 10.13 (High Sierra)	cosmosR_1.2.0.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 3.14	Source Archive