decoupleR
This is thereleased version of decoupleR; for the devel version, seedecoupleR.
decoupleR: Ensemble of computational methods to infer biological activities from omics data
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("decoupleR")| 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression,FunctionalGenomics,GeneExpression,GeneRegulation,Network,Software,StatisticalMethod,Transcription |
| Version | 2.16.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 years) |
| License | GPL-3 + fileLICENSE |
| 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,SmartPhos |
| Suggests Me | SCpubr |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | decoupleR_2.16.0.tar.gz |
| Windows Binary (x86_64) | decoupleR_2.16.0.zip |
| macOS Binary (x86_64) | decoupleR_2.16.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/decoupleR/ |
| Package Short Url | https://bioconductor.org/packages/decoupleR/ |
| Package Downloads Report | Download Stats |