Analysis tools: tl

scmorph can perform trajectory analysis using the Slingshot algorithm. Additionally, it can compute the single-cell distance between treatments and control cell, which can be used for hit calling.

get_ks(adata[, treatment_key, well_key, ...])	Performs the KS test for all treatments and establishes a KS cutoff based on control wells FDR.
slingshot(adata[, cluster_labels, ...])	Trajectory inference using Slingshot
test_common_trajectory(adata, conditions[, ...])	Test for common trajectory using condiments' topologyTest
test_differential_differentiation(adata, ...)	Test for differential differentiation using condiments' differentiationTest
test_differential_progression(adata, conditions)	Test for differential progression using condiments' progressionTest