SNPchip

DOI: 10.18129/B9.bioc.SNPchip    

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

Visualizations for copy number alterations

Bioconductor version: Development (3.9)

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>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SNPchip", version = "3.9")

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 2.29.0
In Bioconductor since BioC 2.0 (R-2.5) (11.5 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_2.29.0.tar.gz
Windows Binary SNPchip_2.29.0.zip
Mac OS X 10.11 (El Capitan) SNPchip_2.29.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: