CINdex: Chromosome Instability Index

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.

AuthorLei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan, Yuriy Gusev
Date of publicationNone
MaintainerYuriy Gusev <yg63@georgetown.edu>
LicenseGPL (>= 2)
Version1.2.0

View on Bioconductor

Files

CINdex/DESCRIPTION
CINdex/NAMESPACE
CINdex/R
CINdex/R/cin.core.R CINdex/R/cin.cytobands.R CINdex/R/cin.standard.R CINdex/R/comp.heatmap.R CINdex/R/convert.grl.to.seg.R CINdex/R/cytobands.cin.draw.R CINdex/R/extract.genes.in.cyto.regions.R CINdex/R/heatmap.draw.R CINdex/R/plot.cytobands.R CINdex/R/process.probe.anno.R CINdex/R/process.reference.genome.R CINdex/R/profile.to.segments.R CINdex/R/run.cin.chr.R CINdex/R/run.cin.cyto.R CINdex/R/segments.to.profile.R CINdex/R/ttest.cyto.cin.heatmap.R
CINdex/build
CINdex/build/vignette.rds
CINdex/data
CINdex/data/clin.crc.RData
CINdex/data/cnvgr.18.auto.RData
CINdex/data/cyto.cin4heatmap.RData
CINdex/data/cytobands.cin.RData
CINdex/data/datalist
CINdex/data/geneAnno.RData
CINdex/data/grl.data.RData
CINdex/data/hg18.ucsctrack.RData
CINdex/data/snpgr.18.auto.RData
CINdex/inst
CINdex/inst/NEWS
CINdex/inst/doc
CINdex/inst/doc/CINdex.R
CINdex/inst/doc/CINdex.Rnw
CINdex/inst/doc/CINdex.pdf
CINdex/inst/doc/PrepareInputData.R
CINdex/inst/doc/PrepareInputData.Rmd
CINdex/inst/doc/PrepareInputData.pdf
CINdex/inst/unitTests
CINdex/inst/unitTests/test-run.cin.chr.R
CINdex/man
CINdex/man/clin.crc.Rd CINdex/man/cnvgr.18.auto.Rd CINdex/man/comp.heatmap.Rd CINdex/man/cyto.cin4heatmap.Rd CINdex/man/cytobands.cin.Rd CINdex/man/extract.genes.in.cyto.regions.Rd CINdex/man/geneAnno.Rd CINdex/man/grl.data.Rd CINdex/man/hg18.ucsctrack.Rd CINdex/man/run.cin.chr.Rd CINdex/man/run.cin.cyto.Rd CINdex/man/snpgr.18.auto.Rd CINdex/man/ttest.cyto.cin.heatmap.Rd
CINdex/tests
CINdex/tests/RunTests.R
CINdex/vignettes
CINdex/vignettes/CIN_relapse_VS_nonrelapse_for_unnormalized_dendrogram.pdf
CINdex/vignettes/CINdex.Rnw
CINdex/vignettes/PrepareInputData.Rmd
CINdex/vignettes/barplots.pdf
CINdex/vignettes/biblio.bib
CINdex/vignettes/chr20.png
CINdex/vignettes/hg19ToHg18.over.chain
CINdex/vignettes/output_chr_plots.pdf

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