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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 (3.18)

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 "4.3") 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")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software
Version 1.11.1
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
Linking To
Suggests minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub
System Requirements
Enhances
URL https://github.com/metamaden/recountmethylation
Bug Reports https://github.com/metamaden/recountmethylation/issues
See More
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_1.11.1.tar.gz
Windows Binary recountmethylation_1.11.1.zip
macOS Binary (x86_64) recountmethylation_1.11.1.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/recountmethylation/
Package Short Url https://bioconductor.org/packages/recountmethylation/
Package Downloads Report Download Stats