To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("VanillaICE")

In most cases, you don't need to download the package archive at all.

VanillaICE

   

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see VanillaICE.

A Hidden Markov Model for high throughput genotyping arrays

Bioconductor version: 2.12

Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays

Author: Robert Scharpf <rscharpf at jhsph.edu>, Kevin Scharpf, and Ingo Ruczinski <ingo at jhsph.edu>

Maintainer: Robert Scharpf <rscharpf at jhsph.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("VanillaICE")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VanillaICE")

 

PDF R Script crlmmDownstream
PDF R Script VanillaICE Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Bioinformatics, CopyNumberVariants, GeneticVariability, SNP, Software, Visualization
Version 1.22.0
In Bioconductor since BioC 2.1 (R-2.6) (8.5 years)
License LGPL-2
Depends R (>= 2.14.0)
Imports stats, utils, methods, Biobase, oligoClasses(>= 1.21.12), lattice, IRanges(>= 1.13.22), grid, msm, iterators, foreach, GenomicRanges, matrixStats
LinkingTo
Suggests genomewidesnp6Crlmm(>= 1.0.7), hapmapsnp6, RColorBrewer, genefilter, RSQLite, foreach, RUnit, pd.mapping50k.hind240, SNPchip(>= 2.5.7), doSNOW
SystemRequirements
Enhances DNAcopy, crlmm(>= 1.17.14)
URL
Depends On Me
Imports Me MinimumDistance
Suggests Me oligoClasses
Build Report  

Package Archives

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

Package Source VanillaICE_1.22.0.tar.gz
Windows Binary VanillaICE_1.22.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VanillaICE_1.22.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/VanillaICE/tree/release-2.12
Package Short Url http://bioconductor.org/packages/VanillaICE/
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:

Fred Hutchinson Cancer Research Center