AUCell

DOI: 10.18129/B9.bioc.AUCell    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see AUCell.

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Bioconductor version: 3.14

AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

Author: Sara Aibar, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium.

Maintainer: Sara Aibar <sara.aibar at kuleuven.vib.be>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AUCell")

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("AUCell")

 

HTML	R Script	AUCell: Identifying cells with active gene sets
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneSetEnrichment, Normalization, SingleCell, Software, Transcription, Transcriptomics, WorkflowStep
Version	1.16.0
In Bioconductor since	BioC 3.6 (R-3.4) (4.5 years)
License	GPL-3
Depends
Imports	data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, S4Vectors, utils
LinkingTo
Suggests	Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo
SystemRequirements
Enhances	doMC, doRNG, doParallel, foreach
URL	http://scenic.aertslab.org
Depends On Me	OSCA.basic
Imports Me	RcisTarget
Suggests Me	decoupleR
Links To Me
Build Report

Package Archives

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

Source Package	AUCell_1.16.0.tar.gz
Windows Binary	AUCell_1.16.0.zip
macOS 10.13 (High Sierra)	AUCell_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AUCell
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AUCell
Package Short Url	https://bioconductor.org/packages/AUCell/
Package Downloads Report	Download Stats