Package: AUCell
Type: Package
Title: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq
        data (e.g. identify cells with specific gene signatures)
Version: 1.33.0
Date: 2024-03-09
Author: Sara Aibar, Stein Aerts. Laboratory of Computational Biology.
        VIB-KU Leuven Center for Brain & Disease Research. Leuven,
        Belgium.
Maintainer: Gert Hulselmans <Gert.Hulselmans@kuleuven.be>
Description: 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.
URL: http://scenic.aertslab.org
Imports: DelayedArray, DelayedMatrixStats, data.table, graphics,
        grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats,
        SummarizedExperiment, BiocGenerics, utils
Enhances: doMC, doRNG, doParallel, foreach
Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery,
        knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne,
        testthat, zoo
License: GPL-3
biocViews: SingleCell, GeneSetEnrichment, Transcriptomics,
        Transcription, GeneExpression, WorkflowStep, Normalization
VignetteBuilder: knitr
RoxygenNote: 7.2.0
Config/pak/sysreqs: make libicu-dev libpng-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:40:49 UTC
RemoteUrl: https://github.com/bioc/AUCell
RemoteRef: HEAD
RemoteSha: cf450388fc138ff0f9dfdbaf9aa5a94e0aa40c40
NeedsCompilation: no
Packaged: 2025-11-02 14:42:12 UTC; root
Built: R 4.6.0; ; 2025-11-02 14:45:09 UTC; windows
