BPRMeth

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see BPRMeth.

Model higher-order methylation profiles

Bioconductor version: 3.21

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 "4.5") 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 1.34.0

In Bioconductor since BioC 3.4 (R-3.3) (9 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

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Package Archives

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

Source Package BPRMeth_1.34.0.tar.gz

Windows Binary (x86_64) BPRMeth_1.34.0.zip

macOS Binary (x86_64) BPRMeth_1.34.0.tgz

macOS Binary (arm64) BPRMeth_1.34.0.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/

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