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AUCell

This is the development version of AUCell; for the stable 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: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneExpression, GeneSetEnrichment, Normalization, SingleCell, Software, Transcription, Transcriptomics, WorkflowStep
Version 1.25.1
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends
Imports DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils
System Requirements
URL http://scenic.aertslab.org
See More
Suggests Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo
Linking To
Enhances doMC, doRNG, doParallel, foreach
Depends On Me OSCA.basic
Imports Me RcisTarget, scFeatures
Suggests Me decoupleR
Links To Me
Build Report Build Report

Package Archives

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

Source Package AUCell_1.25.1.tar.gz
Windows Binary AUCell_1.25.1.zip
macOS Binary (x86_64) AUCell_1.25.1.tgz
macOS Binary (arm64) AUCell_1.25.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/AUCell
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AUCell
Bioc Package Browser https://code.bioconductor.org/browse/AUCell/
Package Short Url https://bioconductor.org/packages/AUCell/
Package Downloads Report Download Stats