Repitools

Epigenomic tools

Bioconductor version: Release (2.14)

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 R Script Using Repitools for Epigenomic Sequencing Data
PDF   Reference Manual

Details

biocViews DNAMethylation, GeneExpression, MethylSeq, Software
Version 1.10.1
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, GenomicAlignments, 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
Imports Me
Suggests Me metaseqR

Package Downloads

Package Source Repitools_1.10.1.tar.gz
Windows Binary Repitools_1.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Repitools_1.10.0.tgz
Mac OS X 10.9 (Mavericks)
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