methylPipe

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

Base resolution DNA methylation data analysis

Bioconductor version: Development (3.24)

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")):

Mattia Pelizzola, Kamal Kishore. methylPipe: Base resolution DNA methylation data analysis. doi:10.18129/B9.bioc.methylPipe, R package version 1.47.0, https://bioconductor.org/packages/methylPipe.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNAMethylation, MethylSeq, Sequencing, Software
Version	1.47.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 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, r-universe

Package Archives

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

Source Package	methylPipe_1.47.0.tar.gz
Windows Binary (x86_64)	methylPipe_1.47.0.zip
macOS Binary (big-sur-x86_64)	methylPipe_1.47.0.tgz
macOS Binary (sonoma-arm64)	methylPipe_1.47.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylPipe
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylPipe
Package Short Url	https://bioconductor.org/packages/methylPipe/
Package Downloads Report	Download Stats