collapse_probes         Collapse a probe-level expression matrix to
                        gene level
demo_iot_states         Bundled bioIOT demo dataset
fit_iot                 Fit inverse optimal transport feature weights
gsm_id                  Extract GSM ids from CEL filenames
has_cel_file            Inspect a GEO RAW tar without extracting
make_cost               Cost construction, likelihood and feature
                        standardization
pathway_markers         IOT pathway marker genes (8 pathways)
plot_transition_heatmap
                        bioIOT visualisation
runIOT                  Run IOT on a single-cell object
score_pathways          Score bulk-cohort samples on the 8 IOT pathways
simulate_iot_states     Simulate single-cell state-transition data for
                        bioIOT
soft_sinkhorn           Semi-relaxed OT solver and row-conditional
                        transitions
transition_matrix       Transition matrix, pseudotime and state
                        features
