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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 (3.18)

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 uni-heidelberg.de>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
cosmosR tutorial HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics
Version 1.9.1
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-3
Depends R (>= 4.1)
Imports CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR
Linking To
Suggests testthat, knitr, rmarkdown, piano, ggplot2
System Requirements
Enhances
URL https://github.com/saezlab/COSMOSR
Bug Reports https://github.com/saezlab/COSMOSR/issues
See More
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_1.9.1.tar.gz
Windows Binary cosmosR_1.9.1.zip
macOS Binary (x86_64) cosmosR_1.9.1.tgz
macOS Binary (arm64) cosmosR_1.9.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/cosmosR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cosmosR
Bioc Package Browser https://code.bioconductor.org/browse/cosmosR/
Package Short Url https://bioconductor.org/packages/cosmosR/
Package Downloads Report Download Stats