VanillaICE

DOI: 10.18129/B9.bioc.VanillaICE    

This is the development version of VanillaICE; for the stable release version, see VanillaICE.

A Hidden Markov Model for high throughput genotyping arrays

Bioconductor version: Development (3.11)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("VanillaICE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews CopyNumberVariation, Software
Version 1.49.0
In Bioconductor since BioC 2.1 (R-2.6) (12 years)
License LGPL-2
Depends R (>= 3.5.0), BiocGenerics(>= 0.13.6), GenomicRanges(>= 1.27.6), SummarizedExperiment(>= 1.5.3)
Imports Biobase, S4Vectors(>= 0.23.18), 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 oligoClasses
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: