All functions

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