Repitools

DOI: 10.18129/B9.bioc.Repitools    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see Repitools.

Epigenomic tools

Bioconductor version: 3.14

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 <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 (version "4.1") 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")

 

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

Details

biocViews	DNAMethylation, GeneExpression, MethylSeq, Software
Version	1.40.0
In Bioconductor since	BioC 2.9 (R-2.14) (10.5 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, Rsolnp, cluster
LinkingTo
Suggests	ShortRead, BSgenome.Hsapiens.UCSC.hg18
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Repitools_1.40.0.tar.gz
Windows Binary	Repitools_1.40.0.zip
macOS 10.13 (High Sierra)	Repitools_1.40.0.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/
Package Downloads Report	Download Stats