Repitools

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Repitools.

Epigenomic tools


Bioconductor version: 3.9

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, 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 "3.6") 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

Details

biocViews DNAMethylation, GeneExpression, MethylSeq, Software
Version 1.30.0
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(>= 0.17.25), IRanges(>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome(>= 1.47.3), gplots, grid, MASS, gsmoothr, edgeR(>= 3.4.0), DNAcopy, Ringo, aroma.affymetrix, Rsolnp, cluster
System Requirements
URL
See More
Suggests ShortRead, BSgenome.Hsapiens.UCSC.hg18
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Repitools_1.30.0.tar.gz
Windows Binary Repitools_1.30.0.zip
Mac OS X 10.11 (El Capitan) Repitools_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Repitools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Repitools
Bioc Package Browser https://code.bioconductor.org/browse/Repitools/
Package Short Url https://bioconductor.org/packages/Repitools/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive