Repitools

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see Repitools.

Epigenomic tools

Bioconductor version: 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>

Citation (from within R, enter citation("Repitools")):

Installation

To install this package, start R (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("Repitools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Repitools")

Using Repitools for Epigenomic Sequencing Data PDF R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, GeneExpression, MethylSeq, Software

Version 1.24.0

In Bioconductor since BioC 2.9 (R-2.14) (12.5 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

System Requirements

URL

Suggests ShortRead, BSgenome.Hsapiens.UCSC.hg18

Linking To

Enhances

Depends On Me

Imports Me

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Build Report 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

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Repitools

Package Short Url https://bioconductor.org/packages/Repitools/

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Old Source Packages for BioC 3.6 Source Archive