Package: APL
Type: Package
Title: Association Plots
Version: 1.14.0
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/
git_url: https://git.bioconductor.org/packages/APL
git_branch: RELEASE_3_22
git_last_commit: 3bb5ce8
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 02:48:00 UTC; biocbuild
Author: Clemens Kohl [cre, aut],
  Elzbieta Gralinska [aut],
  Martin Vingron [aut]
Maintainer: Clemens Kohl <kohl.clemens@gmail.com>
Built: R 4.5.1; ; 2025-10-30 12:04:17 UTC; unix
