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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 (3.20)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

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 HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription
Version 2.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
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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
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Depends On Me
Imports Me cosmosR, easier, progeny
Suggests Me SCpubr
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Source Package decoupleR_2.11.0.tar.gz
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