methyAnalysis

DOI: 10.18129/B9.bioc.methyAnalysis    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see methyAnalysis.

DNA methylation data analysis and visualization

Bioconductor version: 3.8

The methyAnalysis package aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. The package also includes functions of estimating the methylation levels from Methy-Seq data.

Author: Pan Du, Richard Bourgon

Maintainer: Pan Du <dupan.mail at gmail.com>, Lei Huang <lhuang at bsd.uchicago.edu>, Gang Feng <g-feng at northwestern.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("methyAnalysis")

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("methyAnalysis")

 

PDF	R Script	An Introduction to the methyAnalysis package
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Microarray, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 2.11 (R-2.15) (6.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb, GenomicRanges, Biobase(>= 2.34.0), org.Hs.eg.db
Imports	grDevices, stats, utils, lumi, methylumi, Gviz, genoset, SummarizedExperiment, IRanges, GenomicRanges, VariantAnnotation, rtracklayer, GenomicFeatures, annotate, Biobase(>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel
LinkingTo
Suggests	FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	methylumi
Links To Me
Build Report

Package Archives

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

Source Package	methyAnalysis_1.24.0.tar.gz
Windows Binary	methyAnalysis_1.24.0.zip
Mac OS X 10.11 (El Capitan)	methyAnalysis_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methyAnalysis
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methyAnalysis
Package Short Url	http://bioconductor.org/packages/methyAnalysis/
Package Downloads Report	Download Stats