DOI: 10.18129/B9.bioc.recountmethylation  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see recountmethylation.

Access and analyze public DNA methylation array data compilations

Bioconductor version: 3.16

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")):


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


biocViews DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software
Version 1.8.6
In Bioconductor since BioC 3.12 (R-4.0) (2.5 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats
Suggests minfiData, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub
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