recountmethylation

Access and analyze public DNA methylation array data compilations

Bioconductor version: 3.23 · Package version: 1.22.0

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.

Installation

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

BiocManager::install("recountmethylation")

Details

Maintainer	Sean K Maden <maden@ohsu.edu>
Author	Sean K Maden [cre, aut] (ORCID: <https://orcid.org/0000-0002-2212-4894>), Brian Walsh [aut] (ORCID: <https://orcid.org/0000-0003-0913-1528>), Kyle Ellrott [aut] (ORCID: <https://orcid.org/0000-0002-6573-5900>), Kasper D Hansen [aut] (ORCID: <https://orcid.org/0000-0003-0086-0687>), Reid F Thompson [aut] (ORCID: <https://orcid.org/0000-0003-3661-5296>), Abhinav Nellore [aut] (ORCID: <https://orcid.org/0000-0001-8145-1484>)
License	Artistic-2.0
URL	https://github.com/metamaden/recountmethylation
Bug Reports	https://github.com/metamaden/recountmethylation/issues
Downloads rank	330
Source branch	RELEASE_3_23
biocViews	DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software

Documentation

Download

Source package

Dependencies

Depends: R (>= 4.1)

Imports: minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats

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