decoupleR

DOI: 10.18129/B9.bioc.decoupleR    

This is the development version of decoupleR; for the stable release version, see decoupleR.

decoupleR: Inferring biological activities from omics data using a collection of methods

Bioconductor version: Development (3.15)

Computational methods allow the extraction of mechanistic signatures from omics data based on prior knowledge resources, reducing the dimensionality of the data 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. Using decoupleR, we evaluated the performance of contemporary methods on transcriptomic and phospho-proteomic perturbation experiments.

Author: Pau Badia-i-Mompel [aut] , Jesús Vélez [cre, 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: Jesús Vélez <jvelezmagic at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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 to decoupleR
PDF   Reference Manual

Details

biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription
Version 2.1.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License GPL-3
Depends R (>= 4.0)
Imports broom, dplyr, GSVA, magrittr, Matrix, purrr, rlang, speedglm, stats, stringr, tibble, tidyr, tidyselect, viper, withr, RobustRankAggreg, fgsea(>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger
LinkingTo
Suggests BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, testthat
SystemRequirements
Enhances
URL https://saezlab.github.io/decoupleR/
BugReports https://github.com/saezlab/decoupleR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package decoupleR_2.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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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