methylPipe

DOI: 10.18129/B9.bioc.methylPipe  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see methylPipe.

Base resolution DNA methylation data analysis

Bioconductor version: 3.16

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>

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

Installation

To install this package, start R (version "4.2") 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")

 

PDF R Script methylPipe.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DNAMethylation, MethylSeq, Sequencing, Software
Version 1.32.0
In Bioconductor since BioC 3.0 (R-3.1) (8.5 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
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_1.32.0.tar.gz
Windows Binary methylPipe_1.32.0.zip (64-bit only)
macOS Binary (x86_64) methylPipe_1.32.0.tgz
macOS Binary (arm64) methylPipe_1.32.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: