AUCell

DOI: 10.18129/B9.bioc.AUCell    

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

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("AUCell")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("AUCell", version = "3.8")

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 1.4.0
License GPL-3
Depends
Imports data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, utils
LinkingTo
Suggests Biobase, BiocStyle, devtools, DT, GEOquery, knitr, NMF, plotly, R2HTML, rbokeh, rmarkdown, Rtsne, testthat, zoo
SystemRequirements
Enhances doMC, doRNG, doParallel, foreach
URL http://scenic.aertslab.org
Depends On Me
Imports Me RcisTarget
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package AUCell_1.4.0.tar.gz
Windows Binary AUCell_1.4.0.zip
Mac OS X 10.11 (El Capitan) AUCell_1.4.0.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 http://bioconductor.org/packages/AUCell/
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