Package: bsseq
Version: 1.42.0
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"))
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
Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix,
        doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat
        (>= 1.5.2), 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
NeedsCompilation: yes
RoxygenNote: 7.1.0
git_url: https://git.bioconductor.org/packages/bsseq
git_branch: RELEASE_3_20
git_last_commit: 851185f
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
Packaged: 2024-10-29 23:50:40 UTC; biocbuild
Author: Kasper Daniel Hansen [aut, cre]
    (<https://orcid.org/0000-0003-0086-0687>),
  Peter Hickey [aut]
Maintainer: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Built: R 4.4.2; x86_64-pc-linux-gnu; 'Mon, 13 Jan 2025 23:17:58 +0100'; unix
