build_state_features	transitions
collapse_probes	collapse_probes
demo_iot_states	demo_iot_states
find_platform_file	tar_utils
fit_iot	fit_iot
gsm_id	gsm_id
has_cel_file	tar_utils
make_cost	cost
pathway_markers	pathway_markers
plot_pathway_trend	plot
plot_theta	plot
plot_transition_flow	plot
plot_transition_heatmap	plot
print.bioIOT_fit	fit_iot
pseudotime_from_transition	transitions
row_ce_loss	cost
row_conditional	solver
runIOT	runIOT
runIOT.default	runIOT
runIOT.matrix	runIOT
runIOT.Seurat	runIOT
runIOT.SingleCellExperiment	runIOT
score_pathways	score_pathways
simulate_iot_states	simulate_iot_states
soft_sinkhorn	solver
summary.bioIOT_fit	fit_iot
transition_matrix	transitions
zscore_phi	cost
