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 (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("AUCell")

Documentation

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	1.0.0
License	GPL-3
Depends
Imports	R.utils, utils, graphics, stats, data.table, mixtools, GSEABase, SummarizedExperiment, methods
LinkingTo
Suggests	Biobase, GEOquery, devtools, zoo, DT, NMF, plotly, BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances	doMC, doRNG, doParallel, foreach
URL	http://scenic.aertslab.org
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	AUCell_1.0.0.tar.gz
Windows Binary	AUCell_1.0.0.zip
Mac OS X 10.11 (El Capitan)	AUCell_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AUCell
Package Short Url	http://bioconductor.org/packages/AUCell/
Package Downloads Report	Download Stats