DESCRIPTION

Package: bsseq
Version: 1.43.1
Encoding: UTF-8
Title: Analyze, manage and store whole-genome methylation data
Description: A collection of tools for analyzing and visualizing whole-genome
    methylation data from sequencing. This includes whole-genome bisulfite
    sequencing and Oxford nanopore data.
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
    email = "kasperdanielhansen@gmail.com", comment = c(ORCID = "0000-0003-0086-0687")),
    person("Peter", "Hickey", role = "aut", email = "peter.hickey@gmail.com", comment = c(ORCID = "0000-0002-8153-6258")),
    person("Hervé", "Pagès", role = "ctb"),
    person("Aaron", "Lun", role = "ctb"))
Depends:
    R (>= 4.0),
    methods,
    BiocGenerics,
    GenomicRanges (>= 1.41.5),
    SummarizedExperiment (>= 1.19.5)
Imports:
    IRanges (>= 2.23.9),
    GenomeInfoDb,
    scales,
    stats,
    parallel,
    tools,
    graphics,
    Biobase,
    locfit,
    gtools,
    data.table (>= 1.11.8),
    S4Vectors (>= 0.27.12),
    R.utils (>= 2.0.0),
    DelayedMatrixStats (>= 1.5.2),
    permute,
    limma,
    DelayedArray (>= 0.15.16),
    Rcpp,
    BiocParallel,
    BSgenome,
    Biostrings,
    utils,
    HDF5Array (>= 1.19.11),
    rhdf5,
    beachmat (>= 2.23.2)
Suggests:
    testthat,
    bsseqData,
    BiocStyle,
    rmarkdown,
    knitr,
    Matrix,
    doParallel,
    rtracklayer,
    BSgenome.Hsapiens.UCSC.hg38,
    batchtools
Collate:
    utils.R
    hasGRanges.R
    BSseq-class.R
    BSseqTstat_class.R
    BSseq_utils.R
    combine.R
    read.bismark.R
    read.modbam2bed.R
    read.modkit.R
    BSmooth.R
    BSmooth.tstat.R
    dmrFinder.R
    gof_stats.R
    plotting.R
    fisher.R
    permutations.R
    BSmooth.fstat.R
    BSseqStat_class.R
    getStats.R
    hdf5_utils.R
    DelayedArray_utils.R
    collapseBSseq.R
    FWIRanges-class.R
    FWGRanges-class.R
    findLoci.R
License: Artistic-2.0
VignetteBuilder: knitr
URL: https://github.com/kasperdanielhansen/bsseq
BugReports: https://github.com/kasperdanielhansen/bsseq/issues
biocViews: DNAMethylation
LinkingTo:
    Rcpp,
    beachmat,
    assorthead (>= 1.1.4)
SystemRequirements: C++17
NeedsCompilation: yes
RoxygenNote: 7.1.0