Repitools

Epigenomic tools

Bioconductor version: Release (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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("Repitools")

Documentation

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)
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
Suggests	GenomicRanges, IRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, ShortRead, BSgenome.Hsapiens.UCSC.hg18, rtracklayer
System Requirements
URL
Depends On Me
Imports Me
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Package Downloads

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
Package Downloads Report	Download Stats

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