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 (3.24)
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]
, Attila Gabor [aut]
, Katharina Zirngibl [aut]
Maintainer: Aurélien Dugourd <dugourd at ebi.ac.uk>
citation("cosmosR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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
| Reference Manual |
Details
| biocViews | CellBiology, GeneSignaling, Metabolomics, Network, Pathways, Proteomics, Software, Transcriptomics |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | cosmosR_1.21.0.zip |
| macOS Binary (big-sur-x86_64) | cosmosR_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | cosmosR_1.21.0.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 |