geomeTriD: A R/Bioconductor package for interactive 3D plot of epigenetic data

Overview

The geomeTriD (Three-Dimensional Geometry) Package provides interactive 3D visualization of chromatin structures using the WebGL-based three.js 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.

geomeTriD is available on Bioconductor: https://bioconductor.org/packages/geomeTriD/

Installaton

To install geomeTriD package, start R (version "4.5") and enter:

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

BiocManager::install("geomeTriD")

Development version are available by:

BiocManager::install('jianhong/geomeTriD')

The dependency of this package is R (>= 4.5.0).

Documentation

To view documentation of geomeTriD, start R and enter:

browseVignettes('geomeTriD')

The documentation are also available online at Bioconductor.

A quick-start introduction video is available on YouTube: Youtube Video

Contributions and Support

If you would like to contribute to this package, the standard workflow is as follows:

  1. Check that there isn’t already an issue about your idea in the jianhong/geomeTriD/issues to avoid duplicating work. If there isn’t one already, please create one so that others know you’re working on this
  2. Fork the jianhong/geomeTriD to your GitHub account
  3. Make the necessary changes / additions within your forked repository following Bioconductor contribution
  4. Use devtools::build and devtools::check to check the package work properly.
  5. Submit a Pull Request against the main or current RELEASE_VERSION branch and wait for the code to be reviewed and merged.

If you’re not used to this workflow with git, you can start with some docs from GitHub or even their excellent git resources.

For further information or help, don’t hesitate to get in touch on the Bioconductor support site with tag #geomeTriD or create a new issues at jianhong/geomeTriD/issues.

Reporting bug/issues

Many thanks for taking an interest in improving this package. Please report bug/issues at jianhong/geomeTriD/issues.