VanillaICE
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see VanillaICE.
A Hidden Markov Model for high throughput genotyping arrays
Bioconductor version: 3.9
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 "3.6") 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 | R Script | |
| VanillaICE Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Software |
| Version | 1.46.0 |
| 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 | 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 | CNPBayes, oligoClasses |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VanillaICE_1.46.0.tar.gz |
| Windows Binary | VanillaICE_1.46.0.zip |
| Mac OS X 10.11 (El Capitan) | VanillaICE_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VanillaICE |
| Source Repository (Developer Access) | git clone [email protected]:packages/VanillaICE |
| Bioc Package Browser | https://code.bioconductor.org/browse/VanillaICE/ |
| Package Short Url | https://bioconductor.org/packages/VanillaICE/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |