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

Bioconductor version: Release (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: Gert Hulselmans <Gert.Hulselmans at>

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


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if (!require("BiocManager", quietly = TRUE))


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


biocViews GeneExpression, GeneSetEnrichment, Normalization, SingleCell, Software, Transcription, Transcriptomics, WorkflowStep
Version 1.26.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Imports DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils
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Suggests Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo
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Enhances doMC, doRNG, doParallel, foreach
Depends On Me OSCA.basic
Imports Me epiregulon, escape, RcisTarget, scFeatures
Suggests Me decoupleR, SCpubr
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Source Package AUCell_1.26.0.tar.gz
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