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Bioconductor - Repitools

Repitools

This is the released version of Repitools; for the devel version, see Repitools.

Epigenomic tools

Bioconductor version: Release (3.21)

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 "4.5") 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 1.54.0 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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 System Requirements URL See More Package Archives

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

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