CINdex

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 georgetown.edu>

Installation

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

 

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

Details

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
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, R.utils
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CINdex_1.28.0.tar.gz
Windows Binary	CINdex_1.28.0.zip
macOS Binary (x86_64)	CINdex_1.28.0.tgz
macOS Binary (arm64)	CINdex_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CINdex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CINdex
Bioc Package Browser	https://code.bioconductor.org/browse/CINdex/
Package Short Url	https://bioconductor.org/packages/CINdex/
Package Downloads Report	Download Stats