cosmosR

This is the development version of cosmosR; for the stable release version, see cosmosR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

COSMOS (Causal Oriented Search of Multi-Omic Space)

Bioconductor version: Development (3.24)

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, cre] ORCID: 0000-0002-0714-028X , Attila Gabor [aut] ORCID: 0000-0002-0776-1182 , Katharina Zirngibl [aut] ORCID: 0000-0002-7518-0339

Maintainer: Aurélien Dugourd <dugourd at ebi.ac.uk>

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

Aurélien Dugourd, Attila Gabor, Katharina Zirngibl. cosmosR: COSMOS (Causal Oriented Search of Multi-Omic Space). doi:10.18129/B9.bioc.cosmosR, R package version 1.21.2, https://bioconductor.org/packages/cosmosR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("cosmosR")

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

Documentation

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics
Version	1.21.2
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	CARNIVAL, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR
System Requirements	pandoc (>= 2.8) - https://pandoc.org
URL	https://github.com/saezlab/COSMOSR https://saezlab.github.io/cosmosR/
Bug Reports	https://github.com/saezlab/COSMOSR/issues

Suggests	testthat, knitr, rmarkdown, htmltools, markdown, ggplot2, stringi, reshape2
Linking To
Enhances
Depends On Me
Imports Me	MetaProViz
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)	cosmosR_1.21.2.zip (64-bit only)
macOS Binary (big-sur-x86_64)	cosmosR_1.21.2.tgz
macOS Binary (sonoma-arm64)	cosmosR_1.21.2.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