VanillaICE

A Hidden Markov Model for high throughput genotyping arrays

Bioconductor version: 2.9

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("VanillaICE")

PDF	R Script	Smoothing copy number estimates from crlmm
PDF	R Script	VanillaICE Vignette
PDF		VanillaICE-fig2.pdf
PDF		VanillaICE-fig3.pdf
PDF		VanillaICE-fig5.pdf
PDF		VanillaICE-integerCopynumber.pdf
PDF		VanillaICE-xyplot.pdf
PDF		VanillaICE-xyplotExample.pdf
PDF		Reference Manual

biocViews	Bioinformatics, CopyNumberVariants, SNP, GeneticVariability, Visualization
Depends	R (>= 2.13.0), IRanges, oligoClasses(>= 1.15.40), methods, stats
Imports	SNPchip(>= 1.15.0), stats, Biobase, lattice, utils, IRanges, grid
Suggests	crlmm(>= 1.11.55), genomewidesnp6Crlmm, hapmapsnp6, RColorBrewer, genefilter, RSQLite
System Requirements
License	LGPL-2
URL
Depends On Me
Imports Me
Suggests Me	oligoClasses, SNPchip
Version	1.16.1
Since	Bioconductor 2.1 (R-2.6)

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