BioTrajX: evaluating biological plausibility in single-cell trajectory inference

BioTrajX, an R package, provides three biologically informed metrics—Directionality (D), Order Consistency (O), and Endpoint Validity (E)—to compare single-cell pseudotime trajectories from the same dataset.

• Why it matters: Trajectory inference methods and analysis choices can yield divergent pseudotime orderings, yet existing evaluations often lack standardized ways to incorporate prior biological knowledge.
• What they did: BioTrajX computes Directionality (D) by matching pseudotime to expected progression, Order Consistency (O) by tracking marker-program coherence, and Endpoint Validity (E) by testing enrichment of expected states at endpoints.
• The result: Using these DOE metrics, users can interpretably compare alternative trajectory inference outputs and evaluate root-cell choices before downstream analyses.

AI summary of the abstract · may contain errors · not medical advice · read the paper.