DOI: 10.18129/B9.bioc.CINdex  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CINdex.

Chromosome Instability Index

Bioconductor version: 3.17

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 [aut] (Innovation Center for Biomedical Informatics, Georgetown University Medical Center), Krithika Bhuvaneshwar [aut] (Innovation Center for Biomedical Informatics, Georgetown University Medical Center), Yue Wang [aut, ths] (Virginia Polytechnic Institute and State University), Yuanjian Feng [aut] (Virginia Polytechnic Institute and State University), Ie-Ming Shih [aut] (Johns Hopkins University School of Medicine), Subha Madhavan [aut] (Innovation Center for Biomedical Informatics, Georgetown University Medical Center), Yuriy Gusev [aut, cre] (Innovation Center for Biomedical Informatics, Georgetown University Medical Center)

Maintainer: Yuriy Gusev <yg63 at>

Citation (from within R, enter citation("CINdex")):


To install this package, start R (version "4.3") and enter:

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PDF R Script CINdex Tutorial
PDF R Script How to obtain Cytoband and Stain Information
PDF R Script Prepare input data for CINdex
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH
Version 1.28.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 years)
License GPL (>= 2)
Depends R (>= 3.3), GenomicRanges
Imports bitops, gplots, grDevices, som, dplyr, gridExtra, png, stringr, S4Vectors, IRanges, GenomeInfoDb, graphics, stats, utils
Suggests knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6,, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings, Homo.sapiens, R.utils
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