AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
Bioconductor version: 3.24 · Package version: 1.35.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AUCell")Details
| Maintainer | Gert Hulselmans <Gert.Hulselmans@kuleuven.be> |
| Author | Sara Aibar, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium. |
| License | GPL-3 |
| URL | http://scenic.aertslab.org |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GeneSetEnrichment, Normalization, SingleCell, Software, Transcription, Transcriptomics, WorkflowStep |
| Package Short Url | https://bioconductor.org/packages/AUCell/ |
Citation
From within R, enter citation("AUCell"):
Sara Aibar, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium. AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures). doi:10.18129/B9.bioc.AUCell, R package version 1.35.0, https://bioconductor.org/packages/AUCell.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | AUCell_1.35.0.tar.gz |
| Windows binary (x86_64) | AUCell_1.35.0.zip |
| macOS binary (arm64) | AUCell_1.35.0.tgz |
| macOS binary (x86_64) | AUCell_1.35.0.tgz |
Dependencies
Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils
Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo
Enhances: doMC, doRNG, doParallel, foreach
Reverse dependencies
Imports Me (2): EMTscore, scFeatures
Suggests Me (5): decoupleR, escape, GSABenchmark, pathMED, scDiagnostics