VanillaICE

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see VanillaICE.

A Hidden Markov Model for high throughput genotyping arrays


Bioconductor version: 3.7

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 (version "3.5") and enter:


if (!require("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")
crlmmDownstream PDF R Script
VanillaICE Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, Software
Version 1.42.4
In Bioconductor since BioC 2.1 (R-2.6) (16.5 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
System Requirements
URL
See More
Suggests RUnit, SNPchip, human610quadv1bCrlmm, ArrayTV
Linking To
Enhances doMC, doMPI, doSNOW, doParallel, doRedis
Depends On Me MinimumDistance
Imports Me
Suggests Me oligoClasses
Links To Me
Build Report Build Report

Package Archives

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

Source Package VanillaICE_1.42.4.tar.gz
Windows Binary VanillaICE_1.42.4.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) VanillaICE_1.42.4.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 https://bioconductor.org/packages/VanillaICE/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive