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✨
DESCRIPTION |NEWS
card.svg |card.png
geomeTriD/json (API)

# 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

5.56 score 2 stars 18 scripts 29 exports 166 dependencies

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

Target	Result	Time
bioc-checks	WARNING	382
linux-devel-x86_64	OK	652
source / vignettes	OK	448
linux-release-x86_64	OK	731
macos-release-arm64	OK	360
macos-oldrel-arm64	OK	420
windows-devel	OK	519
windows-release	OK	559
windows-oldrel	OK	561
wasm-release	OK	344

Exports:alignCoor autoK availableGeometries boundaryScore boundaryScoreTAD cellClusters cellDistance compartment create3dGenomicSignals createTADGeometries extractBackbonePositions fill_NA gaussianBlur hierarchicalClusteringTAD loopBouquetPlot mdsPlot pointCluster renderthreeJsViewer rglViewer SDC smooth3dPoints spatialDistanceHeatmap spatialDistanceMatrix SRD threeJsGeometry threejsOutput threeJsViewer view3dCells view3dStructure

Dependencies:abind AnnotationDbi AnnotationFilter aricode askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli clue cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr dbscan DelayedArray deldir dichromat digest dir.expiry dplyr ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 globals glue gridExtra grImport gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph InteractionSet interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle listenv magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl parallelly pillar pkgconfig plotrix png prettyunits progress progressr ProtGenerics purrr R6 RANN rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr rgl rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray strawr stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex trackViewer txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

geomeTriD Vignette: Plot data in 3D

Rendered fromgeomeTriD.Rmdusingknitr::rmarkdown

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

Help page	Topics
Interactive 3D plot of epigenetic data or single cell data	geomeTriD-package geomeTriD
Aligns two sets of genomic with x,y,z	alignCoor
Automate Cluster Number Selection	autoK
Available Geometries	availableGeometries
cluster single cell 3D structures	cellClusters cellDistance
create 3d Geometry by given genomic signals	create3dGenomicSignals
create 3d Geometry by given TADs	createTADGeometries
Extract the backbone coordinates from output of mdsPlot	extractBackbonePositions
fill NA values by upstream and downstream points	fill_NA
Gaussian blur	gaussianBlur
plot GInteractions	loopBouquetPlot
Plot genomic interactions by multi-dimensional scaling plot	mdsPlot
Perform DBSCAN clustering	pointCluster
rgl Viewer View the 3d structure by rgl.	rglViewer
Distance to centroid	SDC
Calculate the smoothed curve for input GRanges	smooth3dPoints
Create the spatial distance matrix	boundaryScore boundaryScoreTAD compartment hierarchicalClusteringTAD spatialDistanceHeatmap spatialDistanceMatrix
Sequence Relabeling Distance	SRD
Class '"threeJsGeometry"'	$,threeJsGeometry-method $<-,threeJsGeometry-method show,threeJsGeometry-method threeJsGeometry threeJsGeometry-class
threeJs Viewer The htmlwidgets viewer for threeJs.	threeJsViewer
Shiny bindings for threeJsViewer	renderthreeJsViewer threejsOutput threeJsViewer-shiny
Plot cell xyz data in 2d or 3d	view3dCells
Plot GRanges xyz data in 2d or 3d	view3dStructure

Package: geomeTriD 1.7.0

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

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Usage by other packages (reverse dependencies)