rGenomeTracks
This is the released version of rGenomeTracks; for the devel version, see rGenomeTracks.
Integerated visualization of epigenomic data
Bioconductor version: Release (3.23)
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("rGenomeTracks")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 |
Details
| biocViews | HiC, Software, Visualization |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | imager, reticulate, methods, rGenomeTracksData |
| System Requirements | pyGenomeTracks (prefered to use install_pyGenomeTracks()) |
| URL |
See More
| Suggests | rmarkdown, knitr, testthat (>= 3.0.0) |
| 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 | rGenomeTracks_1.18.0.tar.gz |
| Windows Binary (x86_64) | rGenomeTracks_1.18.0.zip |
| macOS Binary (big-sur-x86_64) | rGenomeTracks_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | rGenomeTracks_1.18.0.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/ |
| Package Downloads Report | Download Stats |