Reproducibility repository for the CellRank preprint

Code to reproduce results from the CellRank preprint - if you're looking for the reproducibility repository for the final Nature Methods paper, that is here. Please find the main CellRank website at cellrank.org and the preprint at bioRxiv.

Where to find the data

Raw published data for the pancreas, lung and reprogramming examples is available from the Gene Expression Omnibus (GEO) under accession codes GSE132188, GSE141259 and GSE99915, respectively. Processed data, including spliced and unspliced count abundances, is available from figshare. For convenience, the pancreas and lung examples are also available through cellrank.datasets.

Where to find which analysis notebook

You can click the link under figure to open the notebooks in the browser using nbviewer.

figure	notebook path
Fig. 1	notebooks/fig_1_concept/ML-2020-10-13_fig_1_concept.ipynb
Fig. 2	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Fig. 3	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Fig. 4 part-1 part-2	notebooks/fig_4_uncertainty/ML-2020-10-17_fig_4_uncertainty.ipynb and notebooks/suppl_fig_robustness/MK_2020-10-16_robustness.ipynb
Fig. 5 Palantir STEMNET FateID-trends FateID-fate-bias	notebooks/fig_5_benchmarking
Fig. 6	notebooks/fig_6_lung/ML-2020-10-17_fig_6_lung.ipynb
Suppl. Fig. 1	notebooks/suppl_fig_GPCCA/ML-2020-10-17_GPCCA_toy_example.ipynb
Suppl. Fig. 2	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 3	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 4	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 5	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 6 part-1 part-2	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb and notebooks/fig_5_benchmarking/palantir/ML-2020-10-17_palantir.ipynb
Suppl. Fig. 7	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 8	notebooks/suppl_fig_robustness/MK_2020-10-16_robustness.ipynb
Suppl. Fig. 9	notebooks/suppl_fig_robustness/MK_2020-10-16_robustness.ipynb
Suppl. Fig. 10	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 11	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 12	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 13	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb
Suppl. Fig. 14	notebooks/fig_4_uncertainty/ML-2020-10-17_fig_4_uncertainty.ipynb
Suppl. Fig. 15	notebooks/suppl_fig_robustness/MK_2020-10-16_robustness.ipynb
Suppl. Fig. 16	notebooks/suppl_fig_robustness/MK_2020-10-16_robustness.ipynb
Suppl. Fig. 17 part-1 part-2	notebooks/fig_2_pancreas_main/ML-2020-10-14_fig_2_and_3_pancreas_main.ipynb and notebooks/fig_5_benchmarking/palantir/ML-2020-10-17_palantir.ipynb
Suppl. Fig. 18	notebooks/fig_5_benchmarking/fateid/MK_2020-10-17_plot_trends.ipynb
Suppl. Fig. 19	notebooks/fig_5_benchmarking/fateid/MK_2020-10-17_plot_trends.ipynb
Suppl. Fig. 20	notebooks/suppl_fig_memory_benchmark/MK_2020-10-16_suppl_fig_memory_benchmark.ipynb
Suppl. Fig. 21	notebooks/fig_6_lung/ML-2020-10-17_fig_6_lung.ipynb
Suppl. Fig. 22	notebooks/fig_6_lung/ML-2020-10-17_fig_6_lung.ipynb
Suppl. Fig. 23	notebooks/fig_6_lung/ML-2020-10-17_fig_6_lung.ipynb
Suppl. Fig. 24	notebooks/fig_6_lung/ML-2020-10-17_fig_6_lung.ipynb
Suppl. Fig. 25	No notebook, microscopy results, see Online methods
Suppl. Table 1	notebooks/suppl_fig_time_benchmark/MK_2020-10-16_suppl_fig_time_benchmark.ipynb
Suppl. Table 2	notebooks/suppl_fig_memory_benchmark/MK_2020-10-16_suppl_fig_memory_benchmark.ipynb
Suppl. Table 3	notebooks/suppl_fig_memory_benchmark/MK_2020-10-16_suppl_table_memory_benchmark_1_core.ipynb