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
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see CINdex.
Chromosome Instability Index
Bioconductor version: 3.4
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")
| R Script | CINdex Tutorial | |
| R Script | Prepare input data for CINdex | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH |
| Version | 1.2.0 |
| 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_1.2.0.tar.gz |
| Windows Binary | CINdex_1.2.0.zip |
| Mac OS X 10.9 (Mavericks) | CINdex_1.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CINdex/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/CINdex/ |
| Package Downloads Report | Download Stats |
Documentation »
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