Repitools

Epigenomic tools

Bioconductor version: Release (3.18)

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 "4.3") 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	1.48.0
In Bioconductor since	BioC 2.9 (R-2.14) (12.5 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, Ringo, Rsolnp, cluster
System Requirements
URL

Suggests	ShortRead, BSgenome.Hsapiens.UCSC.hg18
Linking To
Enhances
Depends On Me
Imports Me	OutSplice
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_1.48.0.tar.gz
Windows Binary	Repitools_1.48.0.zip (64-bit only)
macOS Binary (x86_64)	Repitools_1.48.0.tgz
macOS Binary (arm64)	Repitools_1.48.0.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