geomeTriD
This is the development version of geomeTriD; for the stable release version, see geomeTriD.
All Bioconductor versions of geomeTriD
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20
A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data
Bioconductor version: 3.24 · Package version: 1.7.1
The geomeTriD (Three-Dimensional Geometry) Package provides interactive 3D visualization of chromatin structures using the WebGL-based 'three.js' (https://threejs.org/) or the rgl rendering library. It is designed to identify and explore spatial chromatin patterns within genomic regions. The package generates dynamic 3D plots and HTML widgets that integrate seamlessly with Shiny applications, enabling researchers to visualize chromatin organization, detect spatial features, and compare structural dynamics across different conditions and data types.
Author: Jianhong Ou [aut, cre] 
, Kenneth Poss [aut, fnd]
Maintainer: Jianhong Ou <jou at morgridge.org>
Citation
From within R, enter citation("geomeTriD"):
Jianhong Ou, Kenneth Poss. geomeTriD: A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data. doi:10.18129/B9.bioc.geomeTriD, R package version 1.7.1, https://bioconductor.org/packages/geomeTriD.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("geomeTriD")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.7.1 |
| License | MIT + file LICENSE |
| URL | https://github.com/jianhong/geomeTriD |
| Bug Reports | https://github.com/jianhong/geomeTriD/issues |
| Last updated | 2026-07-22 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| Downloads rank | 1860 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/geomeTriD/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("geomeTriD")| geomeTriD Vignette: Plot data in 3D | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | geomeTriD_1.7.1.tar.gz |
| Windows binary (x86_64) | geomeTriD_1.7.1.zip |
| macOS binary (arm64) | geomeTriD_1.7.1.tgz |
| macOS binary (x86_64) | geomeTriD_1.7.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/geomeTriD |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/geomeTriD |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.4.0)
Imports: aricode, BiocGenerics, Biostrings, clue, cluster, dbscan, future.apply, Seqinfo, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, progressr, RANN, rgl, rjson, S4Vectors, scales, stats, trackViewer
Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat