Package: QDNAseq
Version: 1.46.0
Title: Quantitative DNA Sequencing for Chromosomal Aberrations
Depends: R (>= 3.1.0)
Imports: graphics, methods, stats, utils, BiocGenerics, Biobase (>=
        2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>=
        1.32.0), Seqinfo, 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
Config/pak/sysreqs: libbz2-dev liblzma-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:18:34 UTC
RemoteUrl: https://github.com/bioc/QDNAseq
RemoteRef: RELEASE_3_22
RemoteSha: 00b06a1bed6007e4e5338dbcc14589d7724c1323
NeedsCompilation: no
Packaged: 2026-02-27 07:40:04 UTC; root
Author: Ilari Scheinin [aut],
  Daoud Sie [aut, cre],
  Henrik Bengtsson [aut],
  Erik van Dijk [ctb]
Maintainer: Daoud Sie <d.sie@vumc.nl>
Built: R 4.5.2; ; 2026-02-27 07:42:05 UTC; windows
