TrAGEDy: Trajectory Alignment of Gene Expression Dynamics

To compare biological processes between conditions, alignment of single cell transcriptomic trajectories can be performed. Current tools place constraints on what data can be aligned. We present Trajectory Alignment of Gene Expression Dynamics (TrAGEDy) which overcomes these constraints, allowing the alignment of asymmetric biological processes. Across simulated and real datasets, TrAGEDy returns correct alignment based on underlying simulated process, where current tools fail. Across different biological contexts, TrAGEDy can capture biologically relevant genes which other differential expression methods fail to detect. TrAGEDy provides a new tool for in-depth analysis of many emerging single cell transcriptomic datasets.