Package: airpart
Title: Differential cell-type-specific allelic imbalance
Version: 1.19.0
Authors@R: 
    c(person(given = "Wancen",
           family = "Mu",
           role = c("aut", "cre"),
           email = "wancen@live.unc.edu",
           comment = c(ORCID = "0000-0002-5061-7581")),
    person(given = "Michael",
           family = "Love",
           role = c("aut", "ctb"),
           comment = c(ORCID = "0000-0001-8401-0545")))
Description: Airpart identifies sets of genes displaying differential
    cell-type-specific allelic imbalance across cell types
    or states, utilizing single-cell allelic counts. It makes use of a
    generalized fused lasso with binomial observations of allelic
    counts to partition cell types by their allelic
    imbalance. Alternatively, a nonparametric method for partitioning
    cell types is offered. The package includes a number of
    visualizations and quality control functions for examining single
    cell allelic imbalance datasets.
License: GPL-2
Depends: R (>= 4.1)
Imports:
    SingleCellExperiment,
    SummarizedExperiment,
    S4Vectors,
    scater,
    stats,
    smurf,
    apeglm (>= 1.13.3),
    emdbook,
    mclust,
    clue,
    dynamicTreeCut,
    matrixStats,
    dplyr,
    plyr,
    ggplot2,
    ComplexHeatmap,
    forestplot,
    RColorBrewer,
    rlang,
    lpSolve,
    grid,
    grDevices,
    graphics,
    utils,
    pbapply
Suggests: 
    knitr,
    rmarkdown,
    roxygen2 (>= 6.0.0),
    testthat (>= 3.0.0),
    gplots,
    tidyr
VignetteBuilder: knitr
biocViews: SingleCell, RNASeq, ATACSeq, ChIPSeq, Sequencing,
    GeneRegulation, GeneExpression,
    Transcription, TranscriptomeVariant,
    CellBiology, FunctionalGenomics,
    DifferentialExpression,
    GraphAndNetwork, Regression, Clustering, QualityControl
Encoding: UTF-8
BugReports: https://github.com/Wancen/airpart/issues
URL: https://github.com/Wancen/airpart
RoxygenNote: 7.2.3
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/airpart
git_branch: devel
git_last_commit: b69681a
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
