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DESCRIPTION
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Package: CINdex
Title: Chromosome Instability Index
Version: 1.19.1
Authors@R: c(
person(given ="Lei", family ="Song", , email ="[email protected]", role = c("aut"),comment="Innovation Center for Biomedical Informatics, Georgetown University Medical Center"),
person(given ="Krithika", family ="Bhuvaneshwar", , email ="[email protected]", 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 ="[email protected]", role = c("aut"),comment="Innovation Center for Biomedical Informatics, Georgetown University Medical Center"),
person(given ="Yuriy", family ="Gusev", , email ="[email protected]", 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, R.utils
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-10-27 22:14:28 UTC; biocbuild
RoxygenNote: 7.1.1
git_url: https://git.bioconductor.org/packages/CINdex
git_branch: master
git_last_commit: ce318c2
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-27