Package: QDNAseq
Version: 1.45.0
Title: Quantitative DNA Sequencing for Chromosomal Aberrations
Depends: R (>= 3.1.0)
Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase
        (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0),
        GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>=
        0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply
        (>= 1.8.1)
Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>=
        0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1),
        parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19,
        QDNAseq.mm10
Description: Quantitative DNA sequencing for chromosomal aberrations.
    The genome is divided into non-overlapping fixed-sized bins, number of
    sequence reads in each counted, adjusted with a simultaneous
    two-dimensional loess correction for sequence mappability and GC
    content, and filtered to remove spurious regions in the genome.
    Downstream steps of segmentation and calling are also implemented via
    packages DNAcopy and CGHcall, respectively.
Authors@R: c(
    person("Ilari", "Scheinin", role="aut"),
    person("Daoud", "Sie", role=c("aut", "cre"), email="d.sie@vumc.nl"),
    person("Henrik", "Bengtsson", role="aut"),
    person("Erik", "van Dijk", role="ctb"))
biocViews: CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation,
        Preprocessing, QualityControl, Sequencing
License: GPL
URL: https://github.com/ccagc/QDNAseq
BugReports: https://github.com/ccagc/QDNAseq/issues
RoxygenNote: 7.3.2
git_url: https://git.bioconductor.org/packages/QDNAseq
git_branch: devel
git_last_commit: 67a492c
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-04-27
NeedsCompilation: no
Packaged: 2025-04-27 21:16:35 UTC; biocbuild
Author: Ilari Scheinin [aut],
  Daoud Sie [aut, cre],
  Henrik Bengtsson [aut],
  Erik van Dijk [ctb]
Maintainer: Daoud Sie <d.sie@vumc.nl>
Built: R 4.5.0; ; 2025-04-28 02:26:26 UTC; unix
