CINdex: Chromosome Instability Index

Share:

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.

Author
Lei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan, Yuriy Gusev
Date of publication
None
Maintainer
Yuriy Gusev <yg63@georgetown.edu>
License
GPL (>= 2)
Version
1.2.0

View on Bioconductor

Man pages

clin.crc
Colon cancer clinical dataset
cnvgr.18.auto
Probe annotation file for Affymetrix Genome Wide Human SNP...
comp.heatmap
A comprehensive heatmap function that plots Chromosome and...
cytobands.cin
Cytoband CIN dataset
cyto.cin4heatmap
Cytoband CIN T-test output
extract.genes.in.cyto.regions
Given an input of cytobands, it outputs a list of genes that...
geneAnno
CDS gene annotation file
grl.data
Output of segmentation algorithm
hg18.ucsctrack
Human reference annotation file
run.cin.chr
Calculate chromosome CIN
run.cin.cyto
Calculate cytoband CIN
snpgr.18.auto
Probe annotation file for Affymetrix Genome Wide Human SNP...
ttest.cyto.cin.heatmap
Performs T test on cytoband level CIN data, and plots heatmap

Files in this package

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