DOI: 10.18129/B9.bioc.decoupleR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see decoupleR.

decoupleR: Ensemble of computational methods to infer biological activities from omics data

Bioconductor version: 3.17

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>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Introduction
HTML R Script Pathway activity activity inference from scRNA-seq
HTML R Script Pathway activity inference in bulk RNA-seq
HTML R Script Transcription factor activity inference from scRNA-seq
HTML R Script Transcription factor activity inference in bulk RNA-seq
PDF   Reference Manual
Text   NEWS


biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription
Version 2.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0)
Imports broom, dplyr, magrittr, Matrix, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr
Suggests glmnet (>= 4.1.0), 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
Depends On Me
Imports Me dorothea, easier, progeny
Suggests Me SCpubr
Links To Me
Build Report  

Package Archives

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

Source Package decoupleR_2.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) decoupleR_2.6.0.tgz
macOS Binary (arm64) decoupleR_2.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: