decoupleR
decoupleR: Ensemble of computational methods to infer biological activities from omics data
Bioconductor version: 3.23 · Package version: 2.17.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("decoupleR")Details
| Maintainer | Pau Badia-i-Mompel <pau.badia@uni-heidelberg.de> |
| Author | Pau Badia-i-Mompel [aut, cre] (ORCID: <https://orcid.org/0000-0002-1004-3923>), Jesús Vélez-Santiago [aut] (ORCID: <https://orcid.org/0000-0001-5128-3838>), Jana Braunger [aut] (ORCID: <https://orcid.org/0000-0003-0820-9987>), Celina Geiss [aut] (ORCID: <https://orcid.org/0000-0002-8740-706X>), Daniel Dimitrov [aut] (ORCID: <https://orcid.org/0000-0002-5197-2112>), Sophia Müller-Dott [aut] (ORCID: <https://orcid.org/0000-0002-9710-1865>), Petr Taus [aut] (ORCID: <https://orcid.org/0000-0003-3764-9033>), Aurélien Dugourd [aut] (ORCID: <https://orcid.org/0000-0002-0714-028X>), Christian H. Holland [aut] (ORCID: <https://orcid.org/0000-0002-3060-5786>), Ricardo O. Ramirez Flores [aut] (ORCID: <https://orcid.org/0000-0003-0087-371X>), Julio Saez-Rodriguez [aut] (ORCID: <https://orcid.org/0000-0002-8552-8976>) |
| License | GPL-3 + file LICENSE |
| URL | https://saezlab.github.io/decoupleR/ |
| Bug Reports | https://github.com/saezlab/decoupleR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, FunctionalGenomics, GeneExpression, GeneRegulation, Network, Software, StatisticalMethod, Transcription |
| Package Short Url | https://bioconductor.org/packages/decoupleR/ |
Citation
From within R, enter citation("decoupleR"):
Pau Badia-i-Mompel, Jesús Vélez-Santiago, Jana Braunger, Celina Geiss, Daniel Dimitrov, Sophia Müller-Dott, Petr Taus, Aurélien Dugourd, Christian H. Holland, Ricardo O. Ramirez Flores, Julio Saez-Rodriguez. decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data. doi:10.18129/B9.bioc.decoupleR, R package version 2.17.0, https://bioconductor.org/packages/decoupleR.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | decoupleR_2.17.0.tar.gz |
| Windows binary (x86_64) | decoupleR_2.17.0.zip |
| macOS binary (x86_64) | decoupleR_2.17.0.tgz |
Dependencies
Depends: R (>= 4.0)
Imports: BiocParallel, broom, dplyr, magrittr, Matrix, parallelly, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr
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