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 3.1 of Bioconductor; for the stable, up-to-date release version, see VanillaICE.

A Hidden Markov Model for high throughput genotyping arrays

Bioconductor version: 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:

## 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 CopyNumberVariation, Software
Version 1.30.1
In Bioconductor since BioC 2.1 (R-2.6) (8.5 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
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/VanillaICE/tree/release-3.1
Package Short Url http://bioconductor.org/packages/VanillaICE/
Package Downloads Report Download Stats

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