decoupleR
This is the development version of decoupleR; for the stable release version, see decoupleR.
decoupleR: Ensemble of computational methods to infer biological activities from omics data
Bioconductor version: Development (3.24)
Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.
Author: Pau Badia-i-Mompel [aut, cre] 
, Jesús Vélez-Santiago [aut] , Jana Braunger [aut] , Celina Geiss [aut] , Daniel Dimitrov [aut] , Sophia Müller-Dott [aut] , Petr Taus [aut] , Aurélien Dugourd [aut] , Christian H. Holland [aut] , Ricardo O. Ramirez Flores [aut] , Julio Saez-Rodriguez [aut]
Maintainer: Pau Badia-i-Mompel <pau.badia at uni-heidelberg.de>
citation("decoupleR")):Pau Badia-i-Mompel, Jesús Vélez-Santiago, Jana Braunger, Celina Geiss, Daniel Dimitrov, Sophia Müller-Dott, Petr Taus, Aurélien Dugourd, Christian H. Holland, Ricardo O. Ramirez Flores, Julio Saez-Rodriguez. decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data. doi:10.18129/B9.bioc.decoupleR, R package version 2.19.0, https://bioconductor.org/packages/decoupleR.
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("decoupleR")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| No vignettes available | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription |
| Version | 2.19.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | BiocParallel, broom, dplyr, magrittr, Matrix, parallelly, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr |
| System Requirements | |
| URL | https://saezlab.github.io/decoupleR/ |
| Bug Reports | https://github.com/saezlab/decoupleR/issues |
See More
| Suggests | glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork, magick |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | cosmosR, easier, GSABenchmark, pathMED, progeny, SmartPhos |
| Suggests Me | SCpubr |
| 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) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/decoupleR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/decoupleR |
| Package Short Url | https://bioconductor.org/packages/decoupleR/ |
| Package Downloads Report | Download Stats |