recountmethylation
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see recountmethylation.
Access and Analyze DNA Methylation Array Databases
Bioconductor version: 3.12
Access cross-study compilations of DNA methylation array databases. Database files can be downloaded and accessed using provided functions. Background about database file types (HDF5 and HDF5-SummarizedExperiment), SummarizedExperiment classes, and examples for data handling, validation, and analyses, can be found in the package vignettes. Note the disclaimer on package load, and consult the main manuscript for further info.
Author: Sean K Maden [cre, aut] 
, Reid F Thompson [aut] , Kasper D Hansen [aut] , Abhinav Nellore [aut]
Maintainer: Sean K Maden <maden at ohsu.edu>
citation("recountmethylation")):
Installation
To install this package, start R (version "4.0") 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")| Data Analyses | R Script | |
| recountmethylation User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, ExperimentHub, MethylationArray, Microarray, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0) |
| Imports | minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl, R.utils, BiocFileCache |
| System Requirements | |
| URL | https://github.com/metamaden/recountmethylation |
| Bug Reports | https://github.com/metamaden/recountmethylation/issues |
See More
| Suggests | 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | recountmethylation_1.0.0.tar.gz |
| Windows Binary | recountmethylation_1.0.0.zip |
| macOS 10.13 (High Sierra) | recountmethylation_1.0.0.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 |
| Old Source Packages for BioC 3.12 | Source Archive |