recountmethylation

DOI: 10.18129/B9.bioc.recountmethylation    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see recountmethylation.

Access and analyze DNA methylation database compilations

Bioconductor version: 3.14

Access cross-study compilations of DNA methylation array databases. Database files can be downloaded and accessed using provided functions. Background about database file types (HDF5 and HDF5-SummarizedExperiment), SummarizedExperiment classes, and examples for data handling, validation, and analyses, can be found in the package vignettes. Note the disclaimer on package load, and consult the main manuscript for further info.

Author: Sean K Maden [cre, aut] , Reid F Thompson [aut] , Kasper D Hansen [aut] , Abhinav Nellore [aut]

Maintainer: Sean K Maden <maden at ohsu.edu>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("recountmethylation")

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("recountmethylation")

 

HTML	R Script	Data Analyses
HTML	R Script	Determine population ancestry from DNAm arrays
HTML	R Script	Nearest neighbors analysis for DNAm arrays
HTML	R Script	Power analysis for DNAm arrays
HTML	R Script	recountmethylation User's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software
Version	1.4.5
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	Artistic-2.0
Depends	R (>= 4.1)
Imports	minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, IlluminaHumanMethylation450kmanifest
LinkingTo
Suggests	knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub
SystemRequirements
Enhances
URL	https://github.com/metamaden/recountmethylation
BugReports	https://github.com/metamaden/recountmethylation/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	recountmethylation_1.4.5.tar.gz
Windows Binary	recountmethylation_1.4.5.zip
macOS 10.13 (High Sierra)	recountmethylation_1.4.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/recountmethylation
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/recountmethylation
Package Short Url	https://bioconductor.org/packages/recountmethylation/
Package Downloads Report	Download Stats