decoupleR

DOI: 10.18129/B9.bioc.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 (3.17)

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 uni-heidelberg.de>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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
Text   LICENSE

Details

biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription
Version 2.5.0
In Bioconductor since BioC 3.13 (R-4.1) (1.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0)
Imports broom, dplyr, magrittr, Matrix, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr
LinkingTo
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
SystemRequirements
Enhances
URL https://saezlab.github.io/decoupleR/
BugReports https://github.com/saezlab/decoupleR/issues
Depends On Me
Imports Me progeny
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package decoupleR_2.5.0.tar.gz
Windows Binary decoupleR_2.5.0.zip
macOS Binary (x86_64) decoupleR_2.5.0.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
Package Short Url https://bioconductor.org/packages/decoupleR/
Package Downloads Report Download Stats

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