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>, Kevin Scharpf, and Ingo Ruczinski <ingo at>

Maintainer: Robert Scharpf <rscharpf at>

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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
Depends On Me
Imports Me
Suggests Me oligoClasses, SNPchip
Version 1.16.1
Since Bioconductor 2.1 (R-2.6)

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MacOS 10.5 (Leopard) binary VanillaICE_1.16.1.tgz
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