VanillaICE

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see VanillaICE.

A Hidden Markov Model for high throughput genotyping arrays

Bioconductor version: 3.17

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")):

To install this package, start R (version "4.3") 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.

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

Version 1.62.0

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

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

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

Windows Binary VanillaICE_1.62.0.zip (64-bit only)

macOS Binary (x86_64) VanillaICE_1.62.0.tgz

macOS Binary (arm64) VanillaICE_1.62.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/VanillaICE

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VanillaICE

Package Downloads Report Download Stats

Old Source Packages for BioC 3.17 Source Archive