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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "geomeTriD" in publications use:'
type: software
license: MIT
title: 'geomeTriD: A R/Bioconductor package for interactive 3D plot of epigenetic
  data or single cell data'
version: 1.6.0
doi: 10.31083/j.fbs1604021
identifiers:
- type: doi
  value: 10.32614/CRAN.package.geomeTriD
- type: doi
  value: 10.1093/bioadv/vbaf299
abstract: 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.
authors:
- family-names: Ou
  given-names: Jianhong
  email: jou@morgridge.org
  orcid: https://orcid.org/0000-0002-8652-2488
- family-names: Poss
  given-names: Kenneth
  email: kposs@morgridge.org
preferred-citation:
  type: article
  title: 'geomeTriD: a Bioconductor package for interactive and integrative visualization
    of 3D structural model with multi-omics data'
  authors:
  - family-names: Ou
    given-names: Jianhong
    email: jou@morgridge.org
    orcid: https://orcid.org/0000-0002-8652-2488
  - family-names: Poss
    given-names: Keeneth D.
  journal: Bioinformatics Advances
  year: '2025'
  month: '11'
  url: https://doi.org/10.1093/bioadv/vbaf299
  doi: 10.31083/j.fbs1604021
  issn: 2635-0041
  abstract: The three-dimensional organization of the genome plays a critical role
    in regulating gene expression by shaping the spatial and temporal interactions
    between regulatory elements. High-throughput chromosome conformation capture (Hi-C)
    technologies, along with immunoprecipitation- or chromatin accessibility-based
    chromatin architecture mapping methods, enable the measurement of chromatin dynamics
    at both bulk and single-cell levels. However, effectively exploring and comparing
    chromatin structures remains challenging, particularly when integrating multiple
    layers of genomic annotation or comparing structural dynamics across conditions.
    While several tools support interactive 3D genome visualization, few provide a
    flexible, R-integrated framework that supports custom annotations, side-by-side
    comparison of multiple stages or conditions, and deployment in Shiny applications.
    To address this need, we have developed geomeTriD, an R/Bioconductor package that
    enables interactive visualization of chromatin structures using three.js, supports
    multi-layer annotation, allows parallel comparison of two chromatin states, and
    is compatible with Shiny-based analysis workflows. As multi-omic and spatial genomic
    datasets grow in complexity, GeomeTriD will facilitate the reconstruction and
    comparison of 3D genome structures across conditions, linking chromatin architecture
    to gene regulation, epigenetic states, and cell-state transitions. geomeTriD is
    freely available at https://bioconductor.org/packages/geomeTriD. Supplementary
    data are available at Bioinformatics Advances online.
  start: vbaf299
  identifiers:
  - type: doi
    value: 10.1093/bioadv/vbaf299
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/jianhong/geomeTriD
commit: 18ae26dac6cb7e675004e48684aeb64f16786ab3
url: https://github.com/jianhong/geomeTriD
date-released: '2026-04-28'
contact:
- family-names: Ou
  given-names: Jianhong
  email: jou@morgridge.org
  orcid: https://orcid.org/0000-0002-8652-2488