To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("VanillaICE")

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

VanillaICE

 

A Hidden Markov Model for high throughput genotyping arrays

Bioconductor version: Release (3.1)

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

Author: Robert Scharpf <rscharpf at jhu.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:

source("http://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 CopyNumberVariation, Software
Version 1.30.1
In Bioconductor since BioC 2.1 (R-2.6) (7.5 years)
License LGPL-2
Depends R (>= 3.0.0), BiocGenerics(>= 0.13.6), GenomicRanges(>= 1.19.47)
Imports Biobase, oligoClasses(>= 1.24.0), IRanges(>= 1.14.0), S4Vectors, foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb, crlmm, tools
LinkingTo
Suggests RUnit, SNPchip, human610quadv1bCrlmm, BSgenome.Hsapiens.UCSC.hg18, ArrayTV
SystemRequirements
Enhances doMC, doMPI, doSNOW, doParallel, doRedis
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_1.30.1.tar.gz
Windows Binary VanillaICE_1.30.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VanillaICE_1.30.1.tgz
Mac OS X 10.9 (Mavericks) VanillaICE_1.30.1.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center