DESCRIPTION

Package: ChrAccR
Title: Analyzing chromatin accessibility data in R
Description: Tools for analyzing chromatin accessibility data in R. Bulk and single-cell ATAC-seq data are supported.
Authors@R: person("Fabian", "Mueller", email = "muellerf@stanford.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5809-2321"))
Date: 2023-03-08
Suggests:
    ChrAccRex,
    muReportR,
    DelayedArray,
    HDF5Array,
    chromVAR,
    motifmatchr,
    chromVARmotifs,
    GenomicFeatures,
    Rsamtools,
    Biostrings,
    knitr,
    rmarkdown,
    jsonlite,
    cluster,
    matrixStats,
    preprocessCore,
    R.utils,
    tools,
    grid,
    cowplot,
    uwot,
    rtracklayer,
    DESeq2,
    limma,
    LOLA,
    qvalue,
    TFBSTools,
    seqLogo,
    pheatmap,
    grid,
    circlize,
    ComplexHeatmap,
    grDevices,
    BSgenome.Hsapiens.NCBI.GRCh38,
    BSgenome.Hsapiens.UCSC.hg38,
    BSgenome.Hsapiens.1000genomes.hs37d5,
    BSgenome.Hsapiens.UCSC.hg19,
    BSgenome.Mmusculus.UCSC.mm10,
    BSgenome.Mmusculus.UCSC.mm9,
    JASPAR2018
Imports:
    S4Vectors,
    IRanges,
    GenomeInfoDb,
    GenomicRanges,
    GenomicAlignments,
    SummarizedExperiment,
    ggplot2,
    muLogR,
    muRtools,
    Matrix,
    methods,
    stats,
    utils,
    data.table
License: GPL-2
Version: 0.9.21
Collate:
    'ChrAccR.R'
    'classDefs.R'
    'utils.R'
    'config.R'
    'utils_atac.R'
    'utils_motifs.R'
    'annotation.R'
    'utils_chromVAR.R'
    'utils_filehandling.R'
    'DsAcc-class.R'
    'DsATAC-class.R'
    'DsATACsc-class.R'
    'DsNOMe-class.R'
    'import_atac.R'
    'import_atac_10x.R'
    'import_atac_archr.R'
    'importTools_nome.R'
    'differential_nome.R'
    'differential.R'
    'report_atac_summary.R'
    'report_atac_filtering.R'
    'report_atac_normalization.R'
    'report_atac_exploratory.R'
    'report_atac_differential.R'
    'workflow.R'
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.1.1