Repitools

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see Repitools.

Epigenomic tools

Bioconductor version: 3.19

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 mls.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 mls.uzh.ch>

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

Installation

To install this package, start R (version "4.4") 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	1.50.0
In Bioconductor since	BioC 2.9 (R-2.14) (13 years)
License	LGPL (>= 2)
Depends	R (>= 3.5.0), 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, 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_1.50.0.tar.gz
Windows Binary (x86_64)	Repitools_1.50.0.zip
macOS Binary (x86_64)	Repitools_1.50.0.tgz
macOS Binary (arm64)	Repitools_1.50.0.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