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VanillaICE
A Hidden Markov Model for high throughput genotyping arrays
Bioconductor version: Release (2.9)
Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays
Author: Robert Scharpf, Kevin Scharpf, and Ingo Ruczinski
Maintainer: Robert Scharpf
To install this package, start R and enter:
source("http:///biocLite.R")
biocLite("VanillaICE")
To cite this package in a publication, start R and enter:
citation("VanillaICE")
Documentation
| R Script | Smoothing copy number estimates from crlmm | |
| R Script | VanillaICE Vignette | |
| VanillaICE-fig2.pdf | ||
| VanillaICE-fig3.pdf | ||
| VanillaICE-fig5.pdf | ||
| VanillaICE-integerCopynumber.pdf | ||
| VanillaICE-xyplot.pdf | ||
| VanillaICE-xyplotExample.pdf | ||
| Reference Manual |
Details
| biocViews | Bioinformatics, CopyNumberVariants, SNP, GeneticVariability, Visualization |
| Depends | R, IRanges, oligoClasses, methods, stats |
| Imports | SNPchip, stats, Biobase, lattice, utils, IRanges, grid |
| Suggests | crlmm, genomewidesnp6Crlmm, hapmapsnp6, RColorBrewer, genefilter, RSQLite |
| System Requirements | |
| License | LGPL-2 |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | SNPchip, oligoClasses |
| Version | 1.16.1 |
| Since | Bioconductor 2.1 (R-2.6) |
Package Downloads
| Package Source | VanillaICE_1.16.1.tar.gz |
| Windows Binary | VanillaICE_1.16.1.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | VanillaICE_1.16.1.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Flow Cytometry and other assays
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