To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("methylPipe")

In most cases, you don't need to download the package archive at all.

methylPipe

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see methylPipe.

Base resolution DNA methylation data analysis

Bioconductor version: 3.0

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("methylPipe")

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 1.0.5
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL(>=2)
Depends R (>= 3.1.1), methods, grDevices, graphics, stats, utils, GenomicRanges, 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
Build Report

Package Archives

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

Package Source methylPipe_1.0.5.tar.gz
Windows Binary methylPipe_1.0.5.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) methylPipe_1.0.5.tgz
Mac OS X 10.9 (Mavericks) methylPipe_1.0.5.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/methylPipe/tree/release-3.0
Package Short Url http://bioconductor.org/packages/methylPipe/
Package Downloads Report Download Stats

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