FilterGroundTruth()
Filter the ground truth to only include mechanisms in the base object
LoadCustom()
Load the custom Ligand Receptor database from the user
LoadFantom5()
Load FANTOM5 as ground truth
LoadOmniPath()
Load OmniPath as ground truth
RunCellToCell()
RunCellToCell
RunCellToCellSpatial()
RunCellToCellSpatial
RunCellToNeighborhood()
RunCellToNeighborhood
RunCellToSystem()
RunCellToSystem
RunNICHES()
RunNICHES
RunNeighborhoodToCell()
RunNeighborhoodToCell
RunSystemToCell()
RunSystemToCell
compute_edgelist()
Compute an edgelist based on the spatial coordinates
lr_load()
load the Ligands and Receptors that corresponds to the row names of the input seurat
ncomms8866
fantom5
ncomms8866_human
fantom5 human
ncomms8866_mouse
fantom5 mouse
ncomms8866_pig
fantom5 pig
ncomms8866_rat
fantom5 rat
prepSeurat()
Seurat input preprocessing
return_celltypes()
return cell types