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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 (3.19)

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 ohsu.edu>

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

Installation

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

Reference Manual PDF

Details

biocViews DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software
Version 1.13.2
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
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
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/recountmethylation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/recountmethylation
Package Short Url https://bioconductor.org/packages/recountmethylation/
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