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

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Documentation for package ‘geomeTriD’ version 1.3.15

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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