To install this package, start R and enter:

## try http:// if https:// URLs are not supported

In most cases, you don't need to download the package archive at all.




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

Chromosome Instability Index

Bioconductor version: Development (3.5)

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

Maintainer: Yuriy Gusev <yg63 at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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



PDF R Script CINdex Tutorial
PDF R Script Prepare input data for CINdex
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH
Version 1.3.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
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
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source CINdex_1.3.0.tar.gz
Windows Binary
Mac OS X 10.9 (Mavericks) CINdex_1.3.0.tgz
Subversion source (username/password: readonly)
Git source
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: