methylPipe

DOI: 10.18129/B9.bioc.methylPipe    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see methylPipe.

Base resolution DNA methylation data analysis

Bioconductor version: 3.9

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: Kamal Kishore

Maintainer: Kamal Kishore <kamal.fartiyal84 at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	methylPipe.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DNAMethylation, MethylSeq, Sequencing, Software
Version	1.18.0
In Bioconductor since	BioC 3.0 (R-3.1) (5 years)
License	GPL(>=2)
Depends	R (>= 3.2.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment(>= 0.2.0), Rsamtools
Imports	marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR
SystemRequirements
Enhances
URL
Depends On Me	ListerEtAlBSseq
Imports Me	compEpiTools
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	methylPipe_1.18.0.tar.gz
Windows Binary	methylPipe_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	methylPipe_1.18.0.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