DESCRIPTION

Package: fragCounter
Title: GC mappability correction and segmentation
Version: 0.0.0.9000
Authors@R: person(given = "Marcin", family = "Imielinski", email = "mimielinski@nygenome.org", role = c("aut", "cre"))
Description: GC bias curve is determined by loess regression of read count by GC and mappability scores. Segmentation is done by circular binary segmentation (CBS) algorithm after getting tumor/normal ratios of corrected read counts.
biocViews:
  bioc::3.10/GenomicRanges
  bioc::3.10/GenomeInfoDb
Remotes:
  github::mskilab-org/gUtils,
  github::mskilab-org/bamUtils,
  github::mskilab-org/ffTrack,
  github::mskilab-org/skidb
Depends:
  R (>= 3.4)
Imports:
  bamUtils,
  data.table,
  GenomicRanges (>= 1.8),
  gUtils,
  rtracklayer,
  Biostrings,
  DNAcopy,
  GenomeInfoDb,
  IRanges,
  Rsamtools,
  skidb,
  ffTrack
Suggests:
  testthat,
  covr
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3