Package: geomeTriD 1.1.10
Jianhong Ou
geomeTriD: A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data
geomeTriD (Three Dimensional Geometry Package) create interactive 3D plots using the GL library with the 'three.js' visualization library (https://threejs.org) or the rgl library. In addition to creating interactive 3D plots, the application also generates simplified models in 2D. These 2D models provide a more straightforward visual representation, making it easier to analyze and interpret the data quickly. This functionality ensures that users have access to both detailed three-dimensional visualizations and more accessible two-dimensional views, catering to various analytical needs.
Authors:
geomeTriD_1.1.10.tar.gz
geomeTriD_1.1.10.zip(r-4.5)geomeTriD_1.1.10.zip(r-4.4)
geomeTriD_1.1.10.tgz(r-4.5-any)geomeTriD_1.1.10.tgz(r-4.4-any)
geomeTriD_1.1.10.tar.gz(r-4.5-noble)geomeTriD_1.1.10.tar.gz(r-4.4-noble)
geomeTriD_1.1.10.tgz(r-4.4-emscripten)
geomeTriD.pdf |geomeTriD.html✨
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-1.1.9(bioc 3.21)geomeTriD-1.0.1(bioc 3.20)
Last updated 14 hours agofrom:895bfc6b8e. Checks:7 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Apr 03 2025 |
| R-4.5-win | OK | Apr 03 2025 |
| R-4.5-mac | OK | Apr 03 2025 |
| R-4.5-linux | OK | Apr 03 2025 |
| R-4.4-win | OK | Apr 03 2025 |
| R-4.4-mac | OK | Apr 03 2025 |
| R-4.4-linux | OK | Apr 03 2025 |
Exports:alignCooravailableGeometriescreate3dGenomicSignalsextractBackbonePositionsloopBouquetPlotmdsPlotpointClusterrenderthreeJsViewerrglViewersmooth3dPointsthreeJsGeometrythreejsOutputthreeJsViewerview3dCellsview3dStructure
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrdbscanDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragrImportgtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplotrixpngprettyunitsprogressProtGenericspurrrR6RANNrappdirsRColorBrewerRcppRcppEigenRCurlrestfulrrglrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextrackViewertxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryaml
Readme and manuals
Help Manual
| 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 |
| Available Geometries | availableGeometries |
| create 3d Geometry by given genomic signals | create3dGenomicSignals |
| Extract the backbone coordinates from output of mdsPlot | extractBackbonePositions |
| 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 |
| Calculate the smoothed curve for input GRanges | smooth3dPoints |
| 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 |