recountmethylation

This is the released version of recountmethylation; for the devel version, see recountmethylation.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

Access and analyze public DNA methylation array data compilations

Bioconductor version: Release (3.23)

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")):

Sean K Maden, Brian Walsh, Kyle Ellrott, Kasper D Hansen, Reid F Thompson, Abhinav Nellore. recountmethylation: Access and analyze public DNA methylation array data compilations. doi:10.18129/B9.bioc.recountmethylation, R package version 1.22.0, https://bioconductor.org/packages/recountmethylation.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

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")

Practical uses for CpG annotations	HTML	R Script
Working with DNAm data types	HTML	R Script
Data Analyses	HTML	R Script
Determine population ancestry from DNAm arrays	HTML	R Script
Power analysis for DNAm arrays	HTML	R Script
Nearest neighbors analysis for DNAm arrays	HTML	R Script
recountmethylation User's Guide	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software
Version	1.22.0
In Bioconductor since	BioC 3.12 (R-4.0) (6 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

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, r-universe

Package Archives

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

Source Package	recountmethylation_1.22.0.tar.gz
Windows Binary (x86_64)	recountmethylation_1.22.0.zip
macOS Binary (big-sur-x86_64)	recountmethylation_1.22.0.tgz
macOS Binary (sonoma-arm64)	recountmethylation_1.22.0.tgz
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/
Package Downloads Report	Download Stats