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Access and analyze public DNA methylation array data compilations

Bioconductor version: Release (3.19)

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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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
Practical uses for CpG annotations HTML R Script
recountmethylation User's Guide HTML R Script
Working with DNAm data types HTML R Script
Reference Manual PDF


biocViews DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software
Version 1.14.0
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, basilisk, reticulate, DelayedMatrixStats
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Suggests minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub
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Package Archives

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

Source Package recountmethylation_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) recountmethylation_1.14.0.tgz
macOS Binary (arm64) recountmethylation_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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