Package: epialleleR
Title: Fast, Epiallele-Aware Methylation Reporter
Version: 1.8.1
Authors@R: 
  person(given = "Oleksii",
    family = "Nikolaienko",
    role = c("aut", "cre"),
    email = "oleksii.nikolaienko@gmail.com",
    comment = c(ORCID = "0000-0002-5910-4934"))
CommentMaintainer: Oleksii Nikolaienko <oleksii.nikolaienko@gmail.com>
Description: Epialleles are specific DNA methylation patterns that are
  mitotically and/or meiotically inherited. This package calls hypermethylated
  epiallele frequencies at the level of genomic regions or individual cytosines
  in next-generation sequencing data using binary alignment map (BAM) files as
  an input. Other functionality includes extracting methylation patterns,
  computing the empirical cumulative distribution function for per-read beta
  values, and testing the significance of the association between epiallele
  methylation status and base frequencies at particular genomic positions
  (SNPs).
SystemRequirements: C++17, GNU make
NeedsCompilation: yes
Depends: R (>= 4.1)
Imports: stats, methods, utils, GenomicRanges, BiocGenerics,
        GenomeInfoDb, SummarizedExperiment, VariantAnnotation, stringi,
        data.table, Rcpp
LinkingTo: Rcpp, BH, Rhtslib, zlibbioc
Suggests: RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra
License: Artistic-2.0
URL: https://github.com/BBCG/epialleleR
BugReports: https://github.com/BBCG/epialleleR/issues
Encoding: UTF-8
biocViews: DNAMethylation, Epigenetics, MethylSeq
RoxygenNote: 7.2.3
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/epialleleR
git_branch: RELEASE_3_17
git_last_commit: 82910fb
git_last_commit_date: 2023-08-21
Date/Publication: 2023-08-27
Packaged: 2023-08-28 07:39:04 UTC; biocbuild
Author: Oleksii Nikolaienko [aut, cre]
    (<https://orcid.org/0000-0002-5910-4934>)
Maintainer: Oleksii Nikolaienko <oleksii.nikolaienko@gmail.com>
Built: R 4.3.1; aarch64-apple-darwin20; 2023-08-31 19:34:38 UTC; unix
