recountmethylation

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see recountmethylation.

Access and analyze public DNA methylation array data compilations

DOI: 10.18129/B9.bioc.recountmethylation

Bioconductor version: 3.15

Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.

Author: Sean K Maden [cre, aut] , Brian Walsh [aut] , Kyle Ellrott [aut] , Kasper D Hansen [aut] , Reid F Thompson [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 "4.2") 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 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 HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software

Version 1.6.1

In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)

License Artistic-2.0

Depends R (>= 4.1)

Imports minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, IlluminaHumanMethylation450kmanifest

System Requirements

URL https://github.com/metamaden/recountmethylation

Bug Reports https://github.com/metamaden/recountmethylation/issues

Suggests knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

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Build Report Build Report

Package Archives

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

Source Package recountmethylation_1.6.1.tar.gz

Windows Binary recountmethylation_1.6.1.zip

macOS Binary (x86_64) recountmethylation_1.6.1.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 3.15 Source Archive