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 (3.19)

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 "4.4") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics
Version	1.11.0
In Bioconductor since	BioC 3.13 (R-4.1) (3 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR
System Requirements
URL	https://github.com/saezlab/COSMOSR
Bug Reports	https://github.com/saezlab/COSMOSR/issues

Suggests	testthat, knitr, rmarkdown, piano, ggplot2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)	cosmosR_1.11.0.tgz
macOS Binary (arm64)
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