methyAnalysis

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see methyAnalysis.

DNA methylation data analysis and visualization

DOI: 10.18129/B9.bioc.methyAnalysis

Bioconductor version: 3.10

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>

Citation (from within R, enter citation("methyAnalysis")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")

An Introduction to the methyAnalysis package PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, Microarray, Software, Visualization

Version 1.28.0

In Bioconductor since BioC 2.11 (R-2.15) (11.5 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

System Requirements

URL

Suggests FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me methylumi

Links To Me

Build Report Build Report

Package Archives

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

Source Package methyAnalysis_1.28.0.tar.gz

Windows Binary methyAnalysis_1.28.0.zip

Mac OS X 10.11 (El Capitan) methyAnalysis_1.28.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/methyAnalysis

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methyAnalysis

Bioc Package Browser https://code.bioconductor.org/browse/methyAnalysis/

Package Short Url https://bioconductor.org/packages/methyAnalysis/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.10 Source Archive