methylPipe

This is the released version of methylPipe; for the devel version, see methylPipe.

Base resolution DNA methylation data analysis

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DOI: 10.18129/B9.bioc.methylPipe

Bioconductor version: Release (3.22)

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 iit.it>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("methylPipe")

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("methylPipe")

methylPipe.pdf PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DNAMethylation, MethylSeq, Sequencing, Software

Version 1.44.0

In Bioconductor since BioC 3.0 (R-3.1) (11 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, Seqinfo, S4Vectors

System Requirements

URL

Suggests BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR

Linking To

Enhances

Depends On Me ListerEtAlBSseq

Imports Me compEpiTools

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package methylPipe_1.44.0.tar.gz

Windows Binary (x86_64) methylPipe_1.44.0.zip (64-bit only)

macOS Binary (x86_64) methylPipe_1.44.0.tgz

macOS Binary (arm64) methylPipe_1.44.0.tgz

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

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

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

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

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