Package: CINdex
Title: Chromosome Instability Index
Version: 1.8.0
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,
        GenomeInfoDb,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
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-05-01 00:56:05 UTC; biocbuild
Author: Lei Song,
    Krithika Bhuvaneshwar,
	Yue Wang,
    Yuanjian Feng,
    Ie-Ming Shih,
    Subha Madhavan,
    Yuriy Gusev
Maintainer: Yuriy Gusev <yg63@georgetown.edu>
RoxygenNote: 5.0.1
Built: R 3.4.1; ; 2018-10-13 01:11:33 UTC; unix
