recountmethylation

DOI: 10.18129/B9.bioc.recountmethylation  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see recountmethylation.

Access and analyze public DNA methylation array data compilations

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews	DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software
Version	1.10.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Artistic-2.0
Depends	R (>= 4.1)
Imports	minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache, basilisk, reticulate, DelayedMatrixStats
LinkingTo
Suggests	minfiData, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub
SystemRequirements
Enhances
URL	https://github.com/metamaden/recountmethylation
BugReports	https://github.com/metamaden/recountmethylation/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	recountmethylation_1.10.0.tar.gz
Windows Binary	recountmethylation_1.10.0.zip
macOS Binary (x86_64)	recountmethylation_1.10.0.tgz
macOS Binary (arm64)	recountmethylation_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/recountmethylation
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/recountmethylation
Bioc Package Browser	https://code.bioconductor.org/browse/recountmethylation/
Package Short Url	https://bioconductor.org/packages/recountmethylation/
Package Downloads Report	Download Stats