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Bioconductor - recountmethylation (development version)

recountmethylation

This is the development version of recountmethylation; for the stable release version, see recountmethylation.

Access and analyze public DNA methylation array data compilations

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-2212-4894 , Brian Walsh [aut] ORCID: 0000-0003-0913-1528 , Kyle Ellrott [aut] ORCID: 0000-0002-6573-5900 , Kasper D Hansen [aut] ORCID: 0000-0003-0086-0687 , Reid F Thompson [aut] ORCID: 0000-0003-3661-5296 , Abhinav Nellore [aut] ORCID: 0000-0001-8145-1484

Maintainer: Sean K Maden <maden at ohsu.edu>

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software Version 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License Artistic-2.0 Depends R (>= 4.1) Imports minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats System Requirements URL https://github.com/metamaden/recountmethylation Bug Reports https://github.com/metamaden/recountmethylation/issues See More Suggests minfiData, minfiDataEPIC, 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.

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