Repitools

DOI: 10.18129/B9.bioc.Repitools    

Epigenomic tools

Bioconductor version: Release (3.6)

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 <dario.strbenac at sydney.edu.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:

## 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	R Script	Using Repitools for Epigenomic Sequencing Data
PDF		Reference Manual

Details

biocViews	DNAMethylation, GeneExpression, MethylSeq, Software
Version	1.24.0
In Bioconductor since	BioC 2.9 (R-2.14) (6.5 years)
License	LGPL (>= 2)
Depends	R (>= 3.0.0), methods, BiocGenerics(>= 0.8.0)
Imports	parallel, S4Vectors(>= 0.9.25), IRanges(>= 1.20.0), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome, gplots, grid, MASS, gsmoothr, edgeR(>= 3.4.0), DNAcopy, Ringo, aroma.affymetrix, Rsolnp, cluster
LinkingTo
Suggests	ShortRead, BSgenome.Hsapiens.UCSC.hg18
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.

Source Package	Repitools_1.24.0.tar.gz
Windows Binary	Repitools_1.24.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	Repitools_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Repitools
Package Short Url	http://bioconductor.org/packages/Repitools/
Package Downloads Report	Download Stats