source("http://bioconductor.org/biocLite.R")
biocLite("Repitools")

Repitools

Epigenomic tools

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

source("http://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	1.8.6
In Bioconductor since	BioC 2.9 (R-2.14)
License	LGPL (>= 2)
Depends	R (>= 3.0.0), methods, BiocGenerics(>= 0.8.0)
Imports	IRanges(>= 1.20.0), GenomicRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR(>= 3.4.0), DNAcopy, Ringo, aroma.affymetrix, Rsolnp, parallel, Biostrings, Rsamtools, cluster
Suggests	ShortRead, BSgenome.Hsapiens.UCSC.hg18, rtracklayer
System Requirements
URL
Depends On Me
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Package Archives

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

Package Source	Repitools_1.8.6.tar.gz
Windows Binary	Repitools_1.8.6.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Repitools_1.8.6.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats