Repitools
This package isdeprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.22 of Bioconductor.This package has been removed from Bioconductor.For the last stable, up-to-date release version, seeRepitools.
Epigenomic tools
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DNAMethylation,GeneExpression,MethylSeq,Software |
| Version | 1.56.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (14 years) |
| License | LGPL (>= 2) |
| Depends | R (>= 3.5.0), methods,BiocGenerics(>= 0.8.0) |
| Imports | parallel,S4Vectors(>= 0.17.25),IRanges(>= 2.13.12),Seqinfo,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
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/Repitools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Repitools |
| Package Short Url | https://bioconductor.org/packages/Repitools/ |
| Package Downloads Report | Download Stats |