recountmethylation

DOI: 10.18129/B9.bioc.recountmethylation  

Access and analyze public DNA methylation array data compilations

Bioconductor version: Release (3.16)

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 "4.2") 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 1.8.6
In Bioconductor since BioC 3.12 (R-4.0) (2.5 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_1.8.6.tar.gz
Windows Binary recountmethylation_1.8.6.zip
macOS Binary (x86_64) recountmethylation_1.8.6.tgz
macOS Binary (arm64) recountmethylation_1.8.6.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
Old Source Packages for BioC 3.16 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: