CNPBayes

DOI: 10.18129/B9.bioc.CNPBayes    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CNPBayes.

Bayesian mixture models for copy number polymorphisms

Bioconductor version: 3.9

Bayesian hierarchical mixture models for batch effects and copy number.

Author: Stephen Cristiano, Jacob Carey, and Rob Scharpf

Maintainer: Jacob Carey <jcarey15 at jhu.edu>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("CNPBayes")

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("CNPBayes")

 

PDF	R Script	Implementation of Bayesian mixture models for copy number estimation
PDF	R Script	Overview of CNPBayes package
PDF	R Script	Overview of CNPBayes package
PDF		Reference Manual

Details

biocViews	Bayesian, CopyNumberVariation, Software
Version	1.13.5
In Bioconductor since	BioC 3.2 (R-3.2) (4 years)
License	Artistic-2.0
Depends	R (>= 3.4.0), IRanges, GenomicRanges
Imports	Rcpp (>= 0.12.1), S4Vectors, matrixStats, RColorBrewer, gtools, combinat, GenomeInfoDb(>= 1.11.6), methods, BiocGenerics, graphics, stats, coda, SummarizedExperiment, mclust, reshape2, ggplot2, magrittr, purrr, tidyr, dplyr, tibble, scales, data.table, RcppArmadillo
LinkingTo	Rcpp
Suggests	testthat, knitr, BiocStyle, rmarkdown, BiocCheck, MASS, VanillaICE, tidyverse
SystemRequirements
Enhances
URL	https://github.com/scristia/CNPBayes
BugReports	https://github.com/scristia/CNPBayes/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CNPBayes_1.13.5.tar.gz
Windows Binary	CNPBayes_1.13.5.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	CNPBayes_1.13.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CNPBayes
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNPBayes
Package Short Url	https://bioconductor.org/packages/CNPBayes/
Package Downloads Report	Download Stats