SNPchip

DOI: 10.18129/B9.bioc.SNPchip    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see SNPchip.

Visualizations for copy number alterations

Bioconductor version: 3.8

Functions for plotting SNP array data; maintained for historical reasons

Author: Robert Scharpf <rscharpf at jhu.edu> and Ingo Ruczinski

Maintainer: Robert Scharpf <rscharpf at jhu.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SNPchip")

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("SNPchip")

 

PDF	R Script	Plotting Idiograms
PDF		Reference Manual

Details

biocViews	CopyNumberVariation, GeneticVariability, SNP, Software, Visualization
Version	2.28.0
In Bioconductor since	BioC 2.0 (R-2.5) (12 years)
License	LGPL (>= 2)
Depends	R (>= 2.14.0)
Imports	methods, graphics, lattice, grid, foreach, utils, Biobase, S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, oligoClasses(>= 1.31.1)
LinkingTo
Suggests	crlmm(>= 1.17.14), RUnit
SystemRequirements
Enhances	doSNOW, VanillaICE(>= 1.21.24), RColorBrewer
URL	http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html
Depends On Me	mBPCR
Imports Me	crlmm, phenoTest
Suggests Me	Category, MinimumDistance, oligoClasses, VanillaICE
Links To Me
Build Report

Package Archives

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

Source Package	SNPchip_2.28.0.tar.gz
Windows Binary	SNPchip_2.28.0.zip
Mac OS X 10.11 (El Capitan)	SNPchip_2.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SNPchip
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SNPchip
Package Short Url	http://bioconductor.org/packages/SNPchip/
Package Downloads Report	Download Stats