SNPchip
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SNPchip.
Visualizations for copy number alterations
Bioconductor version: 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 (!require("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")| Plotting Idiograms | R Script | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, GeneticVariability, SNP, Software, Visualization |
| Version | 2.30.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) (17 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) |
| System Requirements | |
| URL | http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html |
See More
| Suggests | crlmm(>= 1.17.14), RUnit |
| Linking To | |
| Enhances | doSNOW, VanillaICE(>= 1.21.24), RColorBrewer |
| Depends On Me | mBPCR |
| Imports Me | crlmm, phenoTest |
| Suggests Me | Category, MinimumDistance, oligoClasses, VanillaICE |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SNPchip_2.30.0.tar.gz |
| Windows Binary | SNPchip_2.30.0.zip |
| Mac OS X 10.11 (El Capitan) | SNPchip_2.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SNPchip |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SNPchip |
| Bioc Package Browser | https://code.bioconductor.org/browse/SNPchip/ |
| Package Short Url | https://bioconductor.org/packages/SNPchip/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |