Repitools

Epigenomic tools

Bioconductor version: 2.9

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, 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>

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
Depends	R (>= 2.13.0), methods
Imports	GenomicRanges, IRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, zoo
Suggests	GenomicRanges, IRanges, BSgenome, gplots, grid, MASS, gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, zoo, ShortRead, BSgenome.Hsapiens.UCSC.hg18
System Requirements
License	LGPL (>= 2)
URL
Depends On Me
Imports Me
Suggests Me
Version	1.0.11
Since	Bioconductor 2.9 (R-2.14)

Package Downloads

Package Source	Repitools_1.0.11.tar.gz
Windows Binary	Repitools_1.0.11.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	Repitools_1.0.11.tgz
Package Downloads Report	Download Stats

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