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rGenomeTracks

Integerated visualization of epigenomic data


Bioconductor version: Release (3.18)

rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.

Author: Omar Elashkar [aut, cre]

Maintainer: Omar Elashkar <omar.i.elashkar at gmail.com>

Citation (from within R, enter citation("rGenomeTracks")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rGenomeTracks")

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("rGenomeTracks")
rGenomeTracks HTML R Script
Reference Manual PDF

Details

biocViews HiC, Software, Visualization
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1.0)
Imports imager, reticulate, methods, rGenomeTracksData
System Requirements pyGenomeTracks (prefered to use install_pyGenomeTracks())
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Suggests rmarkdown, knitr, testthat (>= 3.0.0)
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Package Archives

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

Source Package rGenomeTracks_1.8.0.tar.gz
Windows Binary rGenomeTracks_1.8.0.zip
macOS Binary (x86_64) rGenomeTracks_1.8.0.tgz
macOS Binary (arm64) rGenomeTracks_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rGenomeTracks
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rGenomeTracks
Bioc Package Browser https://code.bioconductor.org/browse/rGenomeTracks/
Package Short Url https://bioconductor.org/packages/rGenomeTracks/
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