Please cite the paper below for the geomeTriD package.

Jianhong Ou, Kenneth D Poss, geomeTriD: a Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data, Bioinformatics Advances, 2025;, vbaf299, https://doi.org/10.1093/bioadv/vbaf299

Corresponding BibTeX entry:

  @Article{,
    title = {geomeTriD: a Bioconductor package for interactive and
      integrative visualization of 3D structural model with multi-omics
      data},
    author = {Jianhong Ou and Keeneth D. Poss},
    journal = {Bioinformatics Advances},
    year = {2025},
    month = {11},
    pages = {vbaf299},
    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.},
  }