Package: rCNV
Type: Package
Title: Detect Copy Number Variants from SNPs Data
Version: 1.5.900
Date: 2026-06-03
Language: en-US
Authors@R: c(person(given="Piyal",family="Karunarathne", email="piyalkarumail@yahoo.com", role = c("aut", "cre"),comment = c(ORCID = "0000-0002-1934-145X")),person(given="Qiujie",family="Zhou", email="qiujie.zhou@ebc.uu.se", role = c("aut"),comment = c(ORCID = "0000-0001-7351-2371")),person("Klaus", "Schliep", email="klaus.schliep@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0003-2941-0161")),person(given="Pascal", family="Milesi", role = "aut",comment = c(ORCID = "0000-0001-8580-4291")))
Maintainer: Piyal Karunarathne <piyalkarumail@yahoo.com>
Description: Functions in this package will import filtered variant
        call format (VCF) files of SNPs data and generate data sets to
        detect copy number variants, visualize them and do downstream
        analyses with copy number variants(e.g. Environmental
        association analyses).
License: AGPL (>= 3)
Imports: data.table, graphics, colorspace, R.utils, qgraph, stringr,
        MASS, parallel, stats, methods, utils, pbapply, stringi,
        extraDistr, fitdistrplus, Rsamtools, Biostrings, GenomicRanges,
        GenomeInfoDb, BiocGenerics, IRanges, S4Vectors, rtracklayer
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
biocViews: GenomicVariation, Sequencing, CopyNumberVariation
Depends: R (>= 3.6.0)
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), covr
VignetteBuilder: knitr
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
URL: https://piyalkarum.github.io/rCNV/,
        https://cran.r-project.org/package=rCNV
Additional_repositories: https://bioconductor.org/packages/release/bioc
BugReports: https://github.com/piyalkarum/rCNV/issues
Packaged: 2026-09-27 10:36:25 UTC; root
Config/pak/sysreqs: cmake libglpk-dev make libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://piyalkarum.r-universe.dev
Date/Publication: 2026-06-04 13:18:28 UTC
RemoteUrl: https://github.com/piyalkarum/rcnv
RemoteRef: HEAD
RemoteSha: 81c225fc0f58fad2b370eba8cf464c1eacb92ccc
NeedsCompilation: no
Author: Piyal Karunarathne [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1934-145X>),
  Qiujie Zhou [aut] (ORCID: <https://orcid.org/0000-0001-7351-2371>),
  Klaus Schliep [aut] (ORCID: <https://orcid.org/0000-0003-2941-0161>),
  Pascal Milesi [aut] (ORCID: <https://orcid.org/0000-0001-8580-4291>)