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
git_url: https://git.bioconductor.org/packages/CINdex
git_branch: RELEASE_3_22
git_last_commit: 98fc64f
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
Packaged: 2025-10-30 02:19:58 UTC; biocbuild
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 4.5.1; ; 2025-10-30 09:19:30 UTC; unix
