decoupleR

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


Bioconductor version: Release (3.19)

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("decoupleR")

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("decoupleR")
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
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription
Version 2.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3.5 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, progeny
Suggests Me SCpubr
Links To Me
Build Report Build Report

Package Archives

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

Source Package decoupleR_2.10.0.tar.gz
Windows Binary decoupleR_2.10.0.zip
macOS Binary (x86_64) decoupleR_2.10.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/decoupleR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/decoupleR
Bioc Package Browser https://code.bioconductor.org/browse/decoupleR/
Package Short Url https://bioconductor.org/packages/decoupleR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive