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methylPipe

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

Base resolution DNA methylation data analysis


Bioconductor version: Development (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 iit.it>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Coverage, DNAMethylation, MethylSeq, Sequencing, Software
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
URL
See More
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_1.37.0.tar.gz
Windows Binary methylPipe_1.37.0.zip
macOS Binary (x86_64) methylPipe_1.37.0.tgz
macOS Binary (arm64) methylPipe_1.37.0.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/
Package Downloads Report Download Stats