CINdex
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see CINdex.
Chromosome Instability Index
Bioconductor version: 3.14
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("CINdex")):
Installation
To install this package, start R (version "4.1") 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 | R Script | |
| How to obtain Cytoband and Stain Information | R Script | |
| Prepare input data for CINdex | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Genetics, GenomicVariation, Microarray, Sequencing, Software, aCGH |
| Version | 1.22.0 |
| 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 |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CINdex_1.22.0.tar.gz |
| Windows Binary | CINdex_1.22.0.zip |
| macOS 10.13 (High Sierra) | CINdex_1.22.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |