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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 (3.19)

Hidden Markov Models for characterizing chromosomal alteration in high throughput SNP arrays.

Author: Robert Scharpf [aut, cre]

Maintainer: Robert Scharpf <rscharpf at jhu.edu>

Citation (from within R, enter citation("VanillaICE")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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

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 1.65.0
In Bioconductor since BioC 2.1 (R-2.6) (16.5 years)
License LGPL-2
Depends R (>= 3.5.0), BiocGenerics(>= 0.13.6), GenomicRanges(>= 1.27.6), SummarizedExperiment(>= 1.5.3)
Imports MatrixGenerics, 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
System Requirements
URL
See More
Suggests RUnit, human610quadv1bCrlmm
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_1.65.0.tar.gz
Windows Binary VanillaICE_1.65.0.zip
macOS Binary (x86_64) VanillaICE_1.65.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/VanillaICE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VanillaICE
Bioc Package Browser https://code.bioconductor.org/browse/VanillaICE/
Package Short Url https://bioconductor.org/packages/VanillaICE/
Package Downloads Report Download Stats