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>

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biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription
Version 2.1.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
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
Suggests BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, testthat
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