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

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Documentation for package ‘geomeTriD’ version 1.3.9

• 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
availableGeometries	Available Geometries
cellClusters	cluster single cell 3D structures
cellDistance	cluster single cell 3D structures
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
geomeTriD	Interactive 3D plot of epigenetic data or single cell data
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.
show-method	Class '"threeJsGeometry"'
smooth3dPoints	Calculate the smoothed curve for input GRanges
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