Package: APL
Type: Package
Title: Association Plots
Version: 1.17.0
Authors@R: 
    c(person(given = "Clemens",
        family = "Kohl",
        role = c("cre", "aut"),
        email = "kohl.clemens@gmail.com"),
    person(given = "Elzbieta",
        family = "Gralinska",
        role = c("aut"),
        email = "gralinska@molgen.mpg.de"),
    person(given = "Martin",
        family = "Vingron",
        role = c("aut"),
        email = "vingron@molgen.mpg.de"))
Description: APL is a package developed for computation of Association
        Plots (AP), a method for visualization and analysis of single
        cell transcriptomics data. The main focus of APL is the
        identification of genes characteristic for individual clusters
        of cells from input data. The package performs correspondence
        analysis (CA) and allows to identify cluster-specific genes
        using Association Plots. Additionally, APL computes the
        cluster-specificity scores for all genes which allows to rank
        the genes by their specificity for a selected cell cluster of
        interest.
biocViews: StatisticalMethod, DimensionReduction, SingleCell,
        Sequencing, RNASeq, GeneExpression
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Imports: Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly,
        SeuratObject, SingleCellExperiment, magrittr,
        SummarizedExperiment, topGO, methods, stats, utils,
        org.Hs.eg.db, org.Mm.eg.db, rlang
Depends: R (>= 4.4.0)
Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran,
        sparseMatrixStats, testthat
Config/testthat/edition: 3
Collate: 'constructor.R' 'CA.R' 'apl.R' 'convert.R' 'generic_methods.R'
        'import_packages.R' 'plot.R' 'utils-pipe.R'
URL: https://vingronlab.github.io/APL/
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:58:26 UTC
RemoteUrl: https://github.com/bioc/APL
RemoteRef: HEAD
RemoteSha: e6c22daf7b21f82a1d1769f01a98e903c6c18f8c
NeedsCompilation: no
Packaged: 2026-05-29 08:55:53 UTC; root
Author: Clemens Kohl [cre, aut],
  Elzbieta Gralinska [aut],
  Martin Vingron [aut]
Maintainer: Clemens Kohl <kohl.clemens@gmail.com>
Built: R 4.6.0; ; 2026-05-29 09:21:32 UTC; windows
