cosmosR
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see cosmosR.
COSMOS (Causal Oriented Search of Multi-Omic Space)
Bioconductor version: 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>
citation("cosmosR")):
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")| cosmosR tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| 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 |
| System Requirements | |
| URL | https://github.com/saezlab/COSMOSR |
| Bug Reports | https://github.com/saezlab/COSMOSR/issues |
See More
| Suggests | testthat, knitr, rmarkdown, piano |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/cosmosR/ |
| Package Short Url | https://bioconductor.org/packages/cosmosR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |