DOI: 10.18129/B9.bioc.methyAnalysis    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of methyAnalysis; for the stable release version, see methyAnalysis.

DNA methylation data analysis and visualization

Bioconductor version: Development (3.13)

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: Lei Huang <lhuang1998 at>

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


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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


biocViews DNAMethylation, Microarray, Software, Visualization
Version 1.33.1
In Bioconductor since BioC 2.11 (R-2.15) (8.5 years)
License Artistic-2.0
Depends R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb(>= 1.22.0), GenomicRanges, Biobase(>= 2.34.0),
Imports grDevices, stats, utils, lumi, methylumi, Gviz, genoset, SummarizedExperiment, IRanges, GenomicRanges, VariantAnnotation, rtracklayer, bigmemoryExtras, GenomicFeatures, annotate, Biobase(>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel
Suggests FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene
Depends On Me
Imports Me
Suggests Me methylumi
Links To Me
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