BPRMeth

Model higher-order methylation profiles

Bioconductor version: Release (3.19)

The BPRMeth package is a probabilistic method to quantify explicit features of methylation profiles, in a way that would make it easier to formally use such profiles in downstream modelling efforts, such as predicting gene expression levels or clustering genomic regions or cells according to their methylation profiles.

Author: Chantriolnt-Andreas Kapourani [aut, cre]

Maintainer: Chantriolnt-Andreas Kapourani <kapouranis.andreas at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("BPRMeth")

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("BPRMeth")

BPRMeth: Model higher-order methylation profiles	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, Clustering, Coverage, DNAMethylation, Epigenetics, FeatureExtraction, GeneExpression, GeneRegulation, Genetics, ImmunoOncology, KEGG, RNASeq, Regression, Sequencing, SingleCell, Software
Version	1.30.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 years)
License	GPL-3 \| file LICENSE
Depends	R (>= 3.5.0), GenomicRanges
Imports	assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle
System Requirements
URL

Suggests	testthat, knitr, rmarkdown
Linking To	Rcpp, RcppArmadillo
Enhances
Depends On Me	Melissa
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	BPRMeth_1.30.0.tar.gz
Windows Binary (x86_64)	BPRMeth_1.30.0.zip
macOS Binary (x86_64)	BPRMeth_1.30.0.tgz
macOS Binary (arm64)	BPRMeth_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BPRMeth
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BPRMeth
Bioc Package Browser	https://code.bioconductor.org/browse/BPRMeth/
Package Short Url	https://bioconductor.org/packages/BPRMeth/
Package Downloads Report	Download Stats