recountmethylation

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see recountmethylation.

Access and Analyze DNA Methylation Array Databases


Bioconductor version: 3.12

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>

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

Installation

To install this package, start R (version "4.0") 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")
Data Analyses PDF R Script
recountmethylation User's Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.0.0)
Imports minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache
System Requirements
URL https://github.com/metamaden/recountmethylation
Bug Reports https://github.com/metamaden/recountmethylation/issues
See More
Suggests knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub
Linking To
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 recountmethylation_1.0.0.tar.gz
Windows Binary recountmethylation_1.0.0.zip
macOS 10.13 (High Sierra) recountmethylation_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/recountmethylation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/recountmethylation
Bioc Package Browser https://code.bioconductor.org/browse/recountmethylation/
Package Short Url https://bioconductor.org/packages/recountmethylation/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive