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Bioconductor - decoupleR

decoupleR

This is the released version of decoupleR; for the devel version, see decoupleR.

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

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-1004-3923 , Jesús Vélez-Santiago [aut] ORCID: 0000-0001-5128-3838 , Jana Braunger [aut] ORCID: 0000-0003-0820-9987 , Celina Geiss [aut] ORCID: 0000-0002-8740-706X , Daniel Dimitrov [aut] ORCID: 0000-0002-5197-2112 , Sophia Müller-Dott [aut] ORCID: 0000-0002-9710-1865 , Petr Taus [aut] ORCID: 0000-0003-3764-9033 , Aurélien Dugourd [aut] ORCID: 0000-0002-0714-028X , Christian H. Holland [aut] ORCID: 0000-0002-3060-5786 , Ricardo O. Ramirez Flores [aut] ORCID: 0000-0003-0087-371X , Julio Saez-Rodriguez [aut] ORCID: 0000-0002-8552-8976

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 "4.5") 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")
Details biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription Version 2.14.0 In Bioconductor since BioC 3.13 (R-4.1) (4 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, pathMED, progeny Suggests Me SCpubr Links To Me Build Report Build Report Package Archives

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

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