methylPipe

DOI: 10.18129/B9.bioc.methylPipe    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

Base resolution DNA methylation data analysis

Bioconductor version: Development (3.15)

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 (!requireNamespace("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

PDF   Reference Manual

Details

biocViews Coverage, DNAMethylation, MethylSeq, Sequencing, Software
Version 1.29.2
In Bioconductor since BioC 3.0 (R-3.1) (7 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
Windows Binary
macOS 10.13 (High Sierra)
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

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