Package: geomeTriD 1.7.0

Jianhong Ou

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

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:Jianhong Ou [aut, cre], Kenneth Poss [aut, fnd]

geomeTriD_1.7.0.tar.gz
geomeTriD_1.7.0.zip(r-4.7)geomeTriD_1.7.0.zip(r-4.6)geomeTriD_1.7.0.zip(r-4.5)
geomeTriD_1.7.0.tgz(r-4.6-any)geomeTriD_1.7.0.tgz(r-4.5-any)
geomeTriD_1.7.0.tar.gz(r-4.7-any)geomeTriD_1.7.0.tar.gz(r-4.6-any)
geomeTriD_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
geomeTriD/json (API)
NEWS

# Install 'geomeTriD' in R:
install.packages('geomeTriD', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jianhong/geometrid/issues

On BioConductor:geomeTriD-1.7.0(bioc 3.24)geomeTriD-1.6.0(bioc 3.23)

visualization

5.40 score 1 stars 18 scripts 303 downloads 29 exports 166 dependencies

Last updated from:8d5b74459a. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING395
linux-devel-x86_64OK873
source / vignettesOK509
linux-release-x86_64OK735
macos-release-arm64OK344
macos-oldrel-arm64OK356
windows-develOK979
windows-releaseOK515
windows-oldrelOK816
wasm-releaseOK267

Exports:alignCoorautoKavailableGeometriesboundaryScoreboundaryScoreTADcellClusterscellDistancecompartmentcreate3dGenomicSignalscreateTADGeometriesextractBackbonePositionsfill_NAgaussianBlurhierarchicalClusteringTADloopBouquetPlotmdsPlotpointClusterrenderthreeJsViewerrglViewerSDCsmooth3dPointsspatialDistanceHeatmapspatialDistanceMatrixSRDthreeJsGeometrythreejsOutputthreeJsViewerview3dCellsview3dStructure

Dependencies:abindAnnotationDbiAnnotationFilteraricodeaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclueclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrdbscanDelayedArraydeldirdichromatdigestdir.expirydplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2globalsgluegridExtragrImportgtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslparallellypillarpkgconfigplotrixpngprettyunitsprogressprogressrProtGenericspurrrR6RANNrappdirsRColorBrewerRcppRcppEigenRCurlrestfulrrglrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextrackViewertxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

geomeTriD Vignette: Plot data in 3D

Jianhong Ou

Rendered fromgeomeTriD.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-07-23
Started: 2024-09-01

Readme and manuals

Help Manual

Help pageTopics
Interactive 3D plot of epigenetic data or single cell datageomeTriD-package geomeTriD
Aligns two sets of genomic with x,y,zalignCoor
Automate Cluster Number SelectionautoK
Available GeometriesavailableGeometries
cluster single cell 3D structurescellClusters cellDistance
create 3d Geometry by given genomic signalscreate3dGenomicSignals
create 3d Geometry by given TADscreateTADGeometries
Extract the backbone coordinates from output of mdsPlotextractBackbonePositions
fill NA values by upstream and downstream pointsfill_NA
Gaussian blurgaussianBlur
plot GInteractionsloopBouquetPlot
Plot genomic interactions by multi-dimensional scaling plotmdsPlot
Perform DBSCAN clusteringpointCluster
rgl Viewer View the 3d structure by rgl.rglViewer
Distance to centroidSDC
Calculate the smoothed curve for input GRangessmooth3dPoints
Create the spatial distance matrixboundaryScore boundaryScoreTAD compartment hierarchicalClusteringTAD spatialDistanceHeatmap spatialDistanceMatrix
Sequence Relabeling DistanceSRD
Class '"threeJsGeometry"'$,threeJsGeometry-method $<-,threeJsGeometry-method show,threeJsGeometry-method threeJsGeometry threeJsGeometry-class
threeJs Viewer The htmlwidgets viewer for threeJs.threeJsViewer
Shiny bindings for threeJsViewerrenderthreeJsViewer threejsOutput threeJsViewer-shiny
Plot cell xyz data in 2d or 3dview3dCells
Plot GRanges xyz data in 2d or 3dview3dStructure