Package: CINdex
Title: Chromosome Instability Index
Version: 1.38.0
Authors@R: c(
    person(given ="Lei", family ="Song", , email ="polosong@gmail.com", role = c("aut"),comment="Innovation Center for Biomedical Informatics, Georgetown University Medical Center"),
    person(given ="Krithika", family ="Bhuvaneshwar", , email ="kb472@georgetown.edu", role = c("aut"),comment="Innovation Center for Biomedical Informatics, Georgetown University Medical Center"),
    person(given ="Yue", family ="Wang", , , role = c("aut","ths"), comment="Virginia Polytechnic Institute and State University"),
    person(given ="Yuanjian", family ="Feng", , , role = c("aut"), comment="Virginia Polytechnic Institute and State University"),
    person(given ="Ie-Ming", family ="Shih", , , role = c("aut"), comment="Johns Hopkins University School of Medicine"),
    person(given ="Subha", family ="Madhavan", , email ="yg63@georgetown.edu", role = c("aut"),comment="Innovation Center for Biomedical Informatics, Georgetown University Medical Center"),
 	person(given ="Yuriy", family ="Gusev", , email ="yg63@georgetown.edu", role = c("aut", "cre"),comment="Innovation Center for Biomedical Informatics, Georgetown University Medical Center"))
Description: The CINdex package addresses important area of
        high-throughput genomic analysis. It allows the automated
        processing and analysis of the experimental DNA copy number
        data generated by Affymetrix SNP 6.0 arrays or similar high
        throughput technologies. It calculates the chromosome
        instability (CIN) index that allows to quantitatively
        characterize genome-wide DNA copy number alterations as a
        measure of chromosomal instability. This package calculates not
        only overall genomic instability, but also instability in terms
        of copy number gains and losses separately at the chromosome
        and cytoband level.
Depends: R (>= 3.3), GenomicRanges
License: GPL (>= 2)
LazyData: true
Imports: bitops,gplots,grDevices,som,
        dplyr,gridExtra,png,stringr,S4Vectors, IRanges,
        Seqinfo,graphics, stats, utils
biocViews: Software, CopyNumberVariation, GenomicVariation, aCGH,
        Microarray, Genetics, Sequencing
Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics,
        AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db,
        biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods,
        Biostrings,Homo.sapiens, R.utils
VignetteBuilder: knitr
NeedsCompilation: no
RoxygenNote: 7.1.1
PackageStatus: Deprecated
Config/pak/sysreqs: libicu-dev libpng-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:31:17 UTC
RemoteUrl: https://github.com/bioc/CINdex
RemoteRef: RELEASE_3_22
RemoteSha: 98fc64f492dab549e17715cf9f8c76b08b341a25
Packaged: 2026-01-23 08:24:33 UTC; root
Author: Lei Song [aut] (Innovation Center for Biomedical Informatics,
    Georgetown University Medical Center),
  Krithika Bhuvaneshwar [aut] (Innovation Center for Biomedical
    Informatics, Georgetown University Medical Center),
  Yue Wang [aut, ths] (Virginia Polytechnic Institute and State
    University),
  Yuanjian Feng [aut] (Virginia Polytechnic Institute and State
    University),
  Ie-Ming Shih [aut] (Johns Hopkins University School of Medicine),
  Subha Madhavan [aut] (Innovation Center for Biomedical Informatics,
    Georgetown University Medical Center),
  Yuriy Gusev [aut, cre] (Innovation Center for Biomedical Informatics,
    Georgetown University Medical Center)
Maintainer: Yuriy Gusev <yg63@georgetown.edu>
Built: R 4.5.2; ; 2026-01-23 08:30:04 UTC; windows
