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This is the development version of CINdex; for the stable release version, see CINdex.

Chromosome Instability Index

Bioconductor version: Development (3.20)

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 "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH
Version 1.33.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>= 2)
Depends R (>= 3.3), GenomicRanges
Imports bitops, gplots, grDevices, som, dplyr, gridExtra, png, stringr, S4Vectors, IRanges, GenomeInfoDb, graphics, stats, utils
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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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Follow Installation instructions to use this package in your R session.

Source Package CINdex_1.33.0.tar.gz
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macOS Binary (x86_64) CINdex_1.33.0.tgz
macOS Binary (arm64) CINdex_1.33.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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