Package: bsseq

 Version: 1.24.2

 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 (>= 1.33.6),
     SummarizedExperiment (>= 1.17.4)

 Imports:

     IRanges (>= 2.22.2),

     GenomeInfoDb,

     scales,
     stats,
     graphics,
     Biobase,
     locfit,
     gtools,

     data.table (>= 1.11.8),

     S4Vectors (>= 0.25.14),

     R.utils (>= 2.0.0),

     DelayedMatrixStats (>= 1.5.2),

     permute,
     limma,

     DelayedArray (>= 0.9.8),

     Rcpp,
     BiocParallel,

     BSgenome,

     Biostrings,

     utils,

     HDF5Array (>= 1.11.9),

     rhdf5

 Suggests:

     testthat,

     bsseqData,

     BiocStyle,

     rmarkdown,

     knitr,

     Matrix,

     doParallel,
     rtracklayer,

     BSgenome.Hsapiens.UCSC.hg38,

     beachmat (>= 1.5.2),

     BatchJobs

 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

 BugReports: https://github.com/kasperdanielhansen/bsseq/issues

 biocViews: DNAMethylation

 SystemRequirements: C++11

 LinkingTo: Rcpp, beachmat

 NeedsCompilation: yes

 RoxygenNote: 7.1.0