Repitools

This is the development version of Repitools; for the stable release version, see Repitools.

Epigenomic tools


Bioconductor version: Development (3.20)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.51.0
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, Rsolnp, cluster
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Suggests ShortRead, BSgenome.Hsapiens.UCSC.hg18
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Package Archives

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

Source Package Repitools_1.51.0.tar.gz
Windows Binary Repitools_1.51.0.zip
macOS Binary (x86_64) Repitools_1.51.0.tgz
macOS Binary (arm64) Repitools_1.51.0.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/
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