Code and evaluation data for Global StationaryOT

This repository contains the precomputed simulation data and preprocessed hematopoiesis datasets used in the paper "Global StationaryOT: Trajectory inference for aging time courses of single-cell snapshots" . These files are provided to enable easy access to the data needed to run our example and benchmarking notebooks, available at: https://github.com/ColeBoyle/global-stationaryOT. full_fitted_integrated_hemo_data_sets.tar.gz contains the integrated hematopoiesis data fit with PBA and StatOT. sparsely_fitted_integrated_hemo_data_sets.tar.gz contains the downsampled hematopoiesis data fit with gStatOT and StatOT. bistable_sim_seed=0.h5ad contains the synthetic data used in our first simulation study, and the example-sim.ipynb notebook. GRN_simulation_dropout=0.5_seed=0.h5ad contains the synthetic data used in our second simulation study. BoolODE_code.tar.gz contains the slightly modfied BoolODE code originally from https://github.com/murali-group/BoolODE used to generate our GRN simulation. PBA_code.tar.gz contains the slightly modified Population Balance (PBA) code from https://github.com/AllonKleinLab/PBA used to run our PBA benchmarks. bistable_validation_sets.tar.gz contains the validation sets used in Figures 3 and 4. GRN_validation_sets.tar.gz contains the validation sets used in Figure 5. global-stationaryOT.tar.gz contains the code used to obtain the results in the paper. The raw hematopoiesis data published by Li et al. (2025) are available at: https://www.ncbi.nlm.nih.gov/geo/query/463acc.cgi?acc=GSE189161.