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Base resolution DNA methylation data analysis

Bioconductor version: Release (3.19)

Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.

Author: Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre]

Maintainer: Mattia Furlan <mattia.furlan at>

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


To install this package, start R (version "4.4") and enter:

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


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:

methylPipe.pdf PDF R Script
Reference Manual PDF


biocViews Coverage, DNAMethylation, MethylSeq, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License GPL(>=2)
Depends R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment(>= 0.2.0), Rsamtools
Imports marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors
System Requirements
See More
Suggests BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR
Linking To
Depends On Me ListerEtAlBSseq
Imports Me compEpiTools
Suggests Me
Links To Me
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Package Archives

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

Source Package methylPipe_1.38.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) methylPipe_1.38.0.tgz
macOS Binary (arm64) methylPipe_1.38.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive