Repitools
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Repitools.
Epigenomic tools
Bioconductor version: 3.9
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("Repitools")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual |
Details
| biocViews | DNAMethylation, GeneExpression, MethylSeq, Software |
| Version | 1.30.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 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, aroma.affymetrix, Rsolnp, cluster |
| System Requirements | |
| URL |
See More
| Suggests | ShortRead, BSgenome.Hsapiens.UCSC.hg18 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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_1.30.0.tar.gz |
| Windows Binary | Repitools_1.30.0.zip |
| Mac OS X 10.11 (El Capitan) | Repitools_1.30.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |