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 <email@example.com>|
|License||GPL (>= 2)|
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