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

## Documentation for package ‘geomeTriD’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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