To install this package, start R and enter:

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

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

Repitools

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see Repitools.

Epigenomic tools

Bioconductor version: 2.12

Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.

Author: Mark Robinson <mark.robinson at imls.uzh.ch>, Dario Strbenac <d.strbenac at garvan.org.au>, Aaron Statham <a.statham at garvan.org.au>, Andrea Riebler <andrea.riebler at math.ntnu.no>

Maintainer: Mark Robinson <mark.robinson at imls.uzh.ch>

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

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Repitools")

PDF		qc-cpgPlot.pdf
PDF		qc-enrPlot.pdf
PDF	R Script	Using Repitools for Epigenomic Sequencing Data
PDF		visualisations-binPlotsHeatmap.pdf
PDF		visualisations-binPlotsLine.pdf
PDF		visualisations-cluPlots3.pdf
PDF		visualisations-profPlots.pdf
PDF		Reference Manual

Details

biocViews	DNAMethylation, GeneExpression, Methylseq, Software
Version	1.6.0
In Bioconductor since	BioC 2.9 (R-2.14) (4.5 years)
License	LGPL (>= 2)
Depends	R (>= 2.13.0), methods, BiocGenerics(>= 0.1.0), GenomicRanges(>= 1.7.8)
Imports	BiocGenerics, IRanges(>= 1.13.5), GenomicRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR(>= 2.99.2), DNAcopy, Ringo, aroma.affymetrix, Rsolnp, snowfall, parallel
LinkingTo
Suggests	GenomicRanges, IRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, ShortRead, BSgenome.Hsapiens.UCSC.hg18, rtracklayer
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source	Repitools_1.6.0.tar.gz
Windows Binary	Repitools_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Repitools_1.6.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/Repitools/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/Repitools/
Package Downloads Report	Download Stats