To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CINdex")

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

CINdex

 

   

Chromosome Instability Index

Bioconductor version: Release (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 georgetown.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CINdex")

Documentation

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

browseVignettes("CINdex")

 

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

Details

biocViews CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH
Version 1.4.0
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
LinkingTo
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
SystemRequirements
Enhances
URL
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_1.4.0.tar.gz
Windows Binary CINdex_1.3.0.zip
Mac OS X 10.11 (El Capitan) CINdex_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CINdex/tree/release-3.5
Package Short Url http://bioconductor.org/packages/CINdex/
Package Downloads Report Download Stats

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