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CINdex

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

Chromosome Instability Index


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH
Version 1.31.0
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, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings, Homo.sapiens, R.utils
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Package Archives

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

Source Package CINdex_1.31.0.tar.gz
Windows Binary CINdex_1.31.0.zip
macOS Binary (x86_64) CINdex_1.31.0.tgz
macOS Binary (arm64) CINdex_1.31.0.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