CNPBayes

This package is for version 3.9 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

DOI: 10.18129/B9.bioc.CNPBayes

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>

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

Installation

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

Implementation of Bayesian mixture models for copy number estimation PDF R Script

Overview of CNPBayes package PDF R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, CopyNumberVariation, Software

Version 1.13.5

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, data.table, RcppArmadillo

System Requirements

URL https://github.com/scristia/CNPBayes

Bug Reports https://github.com/scristia/CNPBayes/issues

Suggests testthat, knitr, BiocStyle, rmarkdown, BiocCheck, MASS, VanillaICE, tidyverse

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_1.13.5.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

Bioc Package Browser https://code.bioconductor.org/browse/CNPBayes/

Package Short Url https://bioconductor.org/packages/CNPBayes/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.9 Source Archive