CNPBayes

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CNPBayes.

Bayesian mixture models for copy number polymorphisms


Bioconductor version: 3.7

Bayesian hierarchical mixture models for batch effects and copy number.

Author: Stephen Cristiano, Robert Scharpf, and Jacob Carey

Maintainer: Jacob Carey <jcarey15 at jhu.edu>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("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")
Identifying Copy Number Polymorphisms 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 R Script
Reference Manual PDF

Details

biocViews Bayesian, CopyNumberVariation, Software
Version 1.10.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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
System Requirements
URL https://github.com/scristia/CNPBayes
Bug Reports https://github.com/scristia/CNPBayes/issues
See More
Suggests testthat, knitr, BiocStyle, rmarkdown, BiocCheck, MASS
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CNPBayes_1.10.0.tar.gz
Windows Binary CNPBayes_1.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) CNPBayes_1.10.0.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
Old Source Packages for BioC 3.7 Source Archive