Tools: `mc.tl`#

Inference of cell-cell contacts, mechanical quantities, communication and crosstalk. Unless noted otherwise, results are written into the AnnData object rather than returned.

Communication inference#

`contact_lr_communication`	Contact-based ligand-receptor communication inference.
`mechanical_communication`	Mechanical cell-cell communication inference.
`biochemical_lr_communication`	Biochemical ligand(diffusive)-receptor cell-cell communication inference.

Aggregation and statistics#

`cluster_communication`	Aggregate a cell-level signal matrix into cluster-cluster communication.
`summarize_cluster`	Mean signal per cluster pair and its permutation p-value.
`signal_enrichment`

Mechanical analysis#

`contact_analysis`	Build the cell triangulation used for contact-level mechanics.
`pressure_analysis`
`signal_direction`	Direction of the signal received by each cell, optionally averaged over a grid.
`signal_tensor`	Signal orientation tensor per grid cell.

Spatial gridding#

Partition cells into a regular square grid.

Crosstalk#

crosstalk_analysis

Signal-TF-target gene crosstalk inference (SigXTalk) [Hou2025].