├── .github └── workflows │ ├── build.yml │ ├── build_docs.yml │ ├── publish_pypi.yml │ └── test.yml ├── .gitignore ├── .gitlab-ci.yml ├── .readthedocs.yml ├── Alayoubi_et_al_2024 ├── 1a_PBMC_dataset.ipynb ├── 1b_PBMC_dataset_covariates.ipynb ├── 2_Heart_dataset.ipynb ├── 3_Covid_dataset.ipynb ├── 4_Human_MI_dataset.ipynb ├── 4b_Human_MI_dataset_covariates.ipynb ├── 5_scatac_atlas_dataset.ipynb ├── 6_Simulation_tests.ipynb ├── 7_Simulations_with_increasing_counts.ipynb ├── 8_benchmarking_plots.ipynb ├── 9_tool_comparison_plots.ipynb ├── README.md ├── data │ ├── covid_counts.tsv │ ├── heart_counts.tsv │ ├── human_MI_counts.tsv │ ├── pbmc_counts.tsv │ └── scATAC_counts.tsv ├── plots │ ├── benchmark_accuracy_heatmap.pdf │ ├── benchmark_hitrate_heatmap.pdf │ ├── benchmark_mean_counts_auroc.pdf │ ├── benchmark_sensitivity_fpr_arcsin.pdf │ ├── benchmark_sensitivity_fpr_logit.pdf │ ├── compare_scanpro_sccoda_difs.pdf │ ├── compare_scanpro_sccoda_null.pdf │ ├── covid_boxplot_arcsin.pdf │ ├── covid_sccoda_fdr.pdf │ ├── covid_stripplot_arcsin.pdf │ ├── covid_stripplot_example.pdf │ ├── covid_stripplot_norep_arcsin.pdf │ ├── covid_stripplot_norep_example.pdf │ ├── covid_tool_comparison.pdf │ ├── difs_10reps_arcsin_bootstrap_comparison.pdf │ ├── difs_10reps_logit_bootstrap_comparison.pdf │ ├── difs_14reps_arcsin_bootstrap_comparison.pdf │ ├── difs_14reps_logit_bootstrap_comparison.pdf │ ├── difs_20reps_arcsin_bootstrap_comparison.pdf │ ├── difs_20reps_logit_bootstrap_comparison.pdf │ ├── difs_2reps_arcsin_bootstrap_comparison.pdf │ ├── difs_2reps_logit_bootstrap_comparison.pdf │ ├── difs_3reps_arcsin_bootstrap_comparison.pdf │ ├── difs_3reps_logit_bootstrap_comparison.pdf │ ├── difs_4reps_arcsin_bootstrap_comparison.pdf │ ├── difs_4reps_logit_bootstrap_comparison.pdf │ ├── difs_5reps_arcsin_bootstrap_comparison.pdf │ ├── difs_5reps_logit_bootstrap_comparison.pdf │ ├── difs_8reps_arcsin_bootstrap_comparison.pdf │ ├── difs_8reps_logit_bootstrap_comparison.pdf │ ├── difs_simulation_2_heatmap.pdf │ ├── difs_simulation_heatmap.pdf │ ├── difs_simulation_norep_arcsin.pdf │ ├── difs_simulation_norep_arcsin_boxplots.pdf │ ├── difs_simulation_norep_logit.pdf │ ├── difs_simulation_norep_logit_boxplots.pdf │ ├── difs_simulation_rep_arcsin.pdf │ ├── difs_simulation_rep_arcsin_boxplots.pdf │ ├── difs_simulation_rep_logit.pdf │ ├── difs_simulation_rep_logit_boxplots.pdf │ ├── difs_simulation_ttest_heatmap.pdf │ ├── heart_boxplot.pdf │ ├── heart_condition_covariate.pdf │ ├── heart_condition_norep_covariate.pdf │ ├── heart_norep_stripplot.pdf │ ├── heart_sample_barplot.pdf │ ├── heart_sccoda_fdr.pdf │ ├── heart_stripplot.pdf │ ├── heart_tool_comparison.pdf │ ├── heart_zone_covariate.pdf │ ├── heart_zone_norep_covariate.pdf │ ├── humanMI_all_samples_counts.pdf │ ├── humanMI_ischaemic_vs_ctrl_heatmap.pdf │ ├── humanMI_norep_all.pdf │ ├── humanMI_norep_myeloid.pdf │ ├── humanMI_rep_all.pdf │ ├── humanMI_rep_myeloid.pdf │ ├── humanMI_scanpro_norep_all_combs.pdf │ ├── humanMI_scanpro_norep_filtered_combs.pdf │ ├── humanMI_scanpro_vs_sccoda.pdf │ ├── humanMI_scanpro_vs_sccoda_combs.pdf │ ├── humanMI_sccoda.pdf │ ├── human_mi_zone_covariate.pdf │ ├── human_mi_zone_covariate_arcsin.pdf │ ├── human_mi_zone_norep_covariate.pdf │ ├── human_mi_zone_norep_covariate_arcsin.pdf │ ├── null_simulation_heatmap.pdf │ ├── null_simulation_norep_arcsin.pdf │ ├── null_simulation_norep_arcsin_boxplots.pdf │ ├── null_simulation_norep_logit.pdf │ ├── null_simulation_norep_logit_boxplots.pdf │ ├── null_simulation_rep_arcsin.pdf │ ├── null_simulation_rep_arcsin_boxplots.pdf │ ├── null_simulation_rep_logit.pdf │ ├── null_simulation_rep_logit_boxplots.pdf │ ├── null_simulation_ttest_heatmap.pdf │ ├── pbmc_Age_covariate.pdf │ ├── pbmc_Sex_covariate.pdf │ ├── pbmc_age_covariate.pdf │ ├── pbmc_age_stripplot.pdf │ ├── pbmc_condition_covariate.pdf │ ├── pbmc_sccoda_fdr.pdf │ ├── pbmc_sex_covariate.pdf │ ├── pbmc_sex_norep_stripplot.pdf │ ├── pbmc_sex_stripplot.pdf │ ├── pbmc_tool_comparison.pdf │ ├── scatac_heart_vs_intestine_vs_muscle_heatmap.pdf │ ├── scatac_norep_arcsin_heart-intestine-muscle.pdf │ ├── scatac_norep_arcsin_heart-intestine-muscle_subset.pdf │ ├── scatac_norep_arcsin_heart-muscle.pdf │ ├── scatac_rep_arcsin_heart-intestine-muscle.pdf │ ├── scatac_rep_arcsin_heart-intestine-muscle_subset.pdf │ ├── scatac_rep_arcsin_heart-muscle.pdf │ └── simulation_sccoda_heatmap.pdf └── results │ ├── benchmark │ ├── benchmark_best_auroc.tsv │ ├── benchmark_hitrates.tsv │ ├── benchmark_stats.tsv │ ├── dif_stats.tsv │ ├── null_stats.tsv │ ├── simulation_results_diff.tsv │ ├── simulation_results_diff_2.tsv │ ├── simulation_results_diff_sccoda.tsv │ ├── simulation_results_null.tsv │ ├── simulation_results_null_sccoda.tsv │ ├── simulation_results_ttest_diff.tsv │ └── simulation_results_ttest_null.tsv │ ├── covid_propeller_rep_arcsin.tsv │ ├── covid_propeller_rep_logit.tsv │ ├── covid_scanpro_norep_arcsin.tsv │ ├── covid_scanpro_norep_logit.tsv │ ├── covid_scanpro_rep_arcsin.tsv │ ├── covid_scanpro_rep_logit.tsv │ ├── covid_sccoda_norep.tsv │ ├── covid_sccoda_rep.tsv │ ├── heart_propeller_rep_arcsin.tsv │ ├── heart_propeller_rep_logit.tsv │ ├── heart_scanpro_norep_arcsin.tsv │ ├── heart_scanpro_norep_logit.tsv │ ├── heart_scanpro_rep_arcsin.tsv │ ├── heart_scanpro_rep_logit.tsv │ ├── heart_sccoda_norep.tsv │ ├── heart_sccoda_rep.tsv │ ├── humanMI_scanpro_all_combs.tsv │ ├── humanMI_scanpro_combs.tsv │ ├── humanMI_scanpro_norep_arcsin.tsv │ ├── humanMI_scanpro_norep_logit.tsv │ ├── humanMI_scanpro_rep_arcsin.tsv │ ├── humanMI_scanpro_rep_logit.tsv │ ├── humanMI_sccoda_combs.tsv │ ├── humanMI_sccoda_norep.tsv │ ├── humanMI_sccoda_rep.tsv │ ├── merged_results.tsv │ ├── pbmc_propeller_rep_arcsin.tsv │ ├── pbmc_propeller_rep_logit.tsv │ ├── pbmc_scanpro_norep_arcsin.tsv │ ├── pbmc_scanpro_norep_logit.tsv │ ├── pbmc_scanpro_rep_arcsin.tsv │ ├── pbmc_scanpro_rep_logit.tsv │ ├── pbmc_sccoda_norep.tsv │ ├── pbmc_sccoda_rep.tsv │ ├── scatac_scanpro_norep.tsv │ ├── scatac_scanpro_norep_arcsin_heart-intestine-muscle.tsv │ ├── scatac_scanpro_norep_arcsin_heart-intestine-muscle_subset.tsv │ ├── scatac_scanpro_norep_arcsin_heart-muscle.tsv │ ├── scatac_scanpro_norep_logit_heart-intestine-muscle.tsv │ ├── scatac_scanpro_norep_logit_heart-muscle.tsv │ ├── scatac_scanpro_rep.tsv │ ├── scatac_scanpro_rep_arcsin_heart-intestine-muscle.tsv │ ├── scatac_scanpro_rep_arcsin_heart-intestine-muscle_subset.tsv │ ├── scatac_scanpro_rep_arcsin_heart-muscle.tsv │ ├── scatac_scanpro_rep_logit_heart-intestine-muscle.tsv │ ├── scatac_scanpro_rep_logit_heart-intestine-muscle_subset.tsv │ └── scatac_scanpro_rep_logit_heart-muscle.tsv ├── CHANGES.rst ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── README.md ├── make.bat ├── required_packages.txt └── source │ ├── API.rst │ ├── changelog.rst │ ├── conf.py │ ├── figures │ ├── .gitkeep │ ├── scanpro_logo.png │ └── scanpro_workflow.png │ ├── index.rst │ ├── install.rst │ ├── 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