CINdex

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see CINdex.

Chromosome Instability Index

Bioconductor version: 3.6

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 georgetown.edu>

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

Installation

To install this package, start R (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CINdex")

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

Documentation

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

browseVignettes("CINdex")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH
Version	1.6.0
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
System Requirements
URL

Suggests	knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings, Homo.sapiens
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package	CINdex_1.6.0.tar.gz
Windows Binary	CINdex_1.5.0.zip
Mac OS X 10.11 (El Capitan)	CINdex_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CINdex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CINdex
Package Short Url	https://bioconductor.org/packages/CINdex/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive