Package: bsseq
Version: 1.17.1
Encoding: UTF-8
Title: Analyze, manage and store bisulfite sequencing data
Description: A collection of tools for analyzing and visualizing bisulfite
    sequencing data.
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
    email = "kasperdanielhansen@gmail.com"),
    person("Peter", "Hickey", role = "aut", email = "peter.hickey@gmail.com"))
Depends:
    R (>= 3.5),
    methods,
    BiocGenerics,
    GenomicRanges (>= 1.29.14),
    SummarizedExperiment (>= 1.9.18)
Imports:
    IRanges (>= 2.11.16),
    GenomeInfoDb,
    scales,
    stats,
    graphics,
    Biobase,
    locfit,
    gtools,
    data.table,
    S4Vectors,
    R.utils (>= 2.0.0),
    DelayedMatrixStats (>= 1.3.6),
    permute,
    limma,
    DelayedArray (>= 0.7.15),
    Rcpp,
    BiocParallel,
    BSgenome,
    Biostrings,
    utils,
    HDF5Array,
    beachmat
Suggests:
    testthat,
    bsseqData,
    BiocStyle,
    rmarkdown,
    knitr,
    Matrix,
    doParallel
Collate:
    utils.R
    hasGRanges.R
    BSseq-class.R
    BSseqTstat_class.R
    BSseq_utils.R
    combine.R
    read.bsmooth.R
    read.bismark.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
LazyData: yes
LazyDataCompression: xz
BugReports: https://github.com/kasperdanielhansen/bsseq/issues
biocViews: DNAMethylation
SystemRequirements: C++11
LinkingTo: Rcpp, Rhdf5lib, beachmat
NeedsCompilation: yes
RoxygenNote: 6.1.0