cosmosR
This is the released version of cosmosR; for the devel version, see cosmosR.
COSMOS (Causal Oriented Search of Multi-Omic Space)
Bioconductor version: Release (3.23)
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] 
, Attila Gabor [aut] , Katharina Zirngibl [aut]
Maintainer: Aurélien Dugourd <dugourd at ebi.ac.uk>
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 1.20.0, 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")
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")| MOFA to COSMOS tutorial | HTML | R Script |
| NCI60 tutorial | HTML | R Script |
| cosmosR tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 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 |
See More
| 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 | cosmosR_1.20.0.tar.gz |
| Windows Binary (x86_64) | cosmosR_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | cosmosR_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | cosmosR_1.20.0.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 |