VanillaICE

DOI: 10.18129/B9.bioc.VanillaICE    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see VanillaICE.

A Hidden Markov Model for high throughput genotyping arrays

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("VanillaICE")

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("VanillaICE")

 

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

Details

biocViews	CopyNumberVariation, Software
Version	1.44.0
In Bioconductor since	BioC 2.1 (R-2.6) (11.5 years)
License	LGPL-2
Depends	R (>= 3.0.0), BiocGenerics(>= 0.13.6), GenomicRanges(>= 1.27.6), SummarizedExperiment(>= 1.5.3)
Imports	Biobase, S4Vectors(>= 0.9.25), IRanges(>= 1.14.0), oligoClasses(>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb(>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18
LinkingTo
Suggests	RUnit, SNPchip, human610quadv1bCrlmm, ArrayTV
SystemRequirements
Enhances	doMC, doMPI, doSNOW, doParallel, doRedis
URL
Depends On Me	MinimumDistance
Imports Me
Suggests Me	CNPBayes, oligoClasses
Links To Me
Build Report

Package Archives

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

Source Package	VanillaICE_1.44.0.tar.gz
Windows Binary	VanillaICE_1.44.0.zip
Mac OS X 10.11 (El Capitan)	VanillaICE_1.44.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VanillaICE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VanillaICE
Package Short Url	http://bioconductor.org/packages/VanillaICE/
Package Downloads Report	Download Stats