Package: ADaCGH2
Version: 2.53.0
Date: 2026-04-14
Title: Analysis of Big Data from aCGH Experiments using Parallel
        Computing and ff Objects
Authors@R: c(
    person("Ramon", "Diaz-Uriarte", email = "rdiaz02@gmail.com",
           role = c("aut", "cre"),
	   comment = c(ORCID = "0000-0002-6637-9039")),
    person("Oscar M.", "Rueda", email = "rueda.om@gmail.com",
           role = "aut"),
    person("Li", "Hsu", email = "lih@fhcrc.org",
           role = "ctb", comment = "Wavelet-based aCGH smoothing code"),
    person("Douglas", "Grove", email = "dgrove@fhcrc.org",
           role = "ctb", comment = "Wavelet-based aCGH smoothing code"),
    person("Barry", "Rowlingson", email = "B.Rowlingson@lancaster.ac.uk",
           role = "ctb", comment = "Imagemap code"),
    person("Erez", "Ben-Yaacov",
           role = "ctb", comment = "HaarSeg code"),
    person("Edwin", "de Jonge", email = "edwindjonge@gmail.com",
           role = "ctb", comment = "Code from ffbase"),
    person("Jan", "Wijffels",
           role = "ctb", comment = "Code from ffbase"),
    person("Jan", "van der Laan",
           role = "ctb", comment = "Code from ffbase")
    )
Depends: R (>= 3.2.0), parallel, ff
Imports: bit, DNAcopy, tilingArray, waveslim, cluster, aCGH
Suggests: CGHregions, Cairo, limma
Enhances: Rmpi, GLAD
Description: Analysis and plotting of array CGH data. Allows usage of
        Circular Binary Segementation, wavelet-based smoothing (both as
        in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM,
        GLAD, CGHseg. Most computations are parallelized (either via
        forking or with clusters, including MPI and sockets clusters)
        and use ff for storing data.
biocViews: Microarray, CopyNumberVariation, aCGH
LazyLoad: Yes
License: GPL (>= 3)
URL: https://github.com/rdiaz02/adacgh2
BugReports: https://github.com/rdiaz02/adacgh2
Config/pak/sysreqs: libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:34:57 UTC
RemoteUrl: https://github.com/bioc/ADaCGH2
RemoteRef: HEAD
RemoteSha: 4432814e44a5ca7adb8dcb0b7d69747a8398e8c1
NeedsCompilation: yes
Packaged: 2026-07-03 14:18:50 UTC; root
Author: Ramon Diaz-Uriarte [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6637-9039>),
  Oscar M. Rueda [aut],
  Li Hsu [ctb] (Wavelet-based aCGH smoothing code),
  Douglas Grove [ctb] (Wavelet-based aCGH smoothing code),
  Barry Rowlingson [ctb] (Imagemap code),
  Erez Ben-Yaacov [ctb] (HaarSeg code),
  Edwin de Jonge [ctb] (Code from ffbase),
  Jan Wijffels [ctb] (Code from ffbase),
  Jan van der Laan [ctb] (Code from ffbase)
Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>