├── .gitignore ├── LICENSE.txt ├── README.md ├── Snakefile ├── config.yaml ├── data ├── .gitignore ├── test.pq └── test.tsv ├── environment.yml ├── job_output └── .gitignore ├── notebooks ├── HLCA_concordance.ipynb ├── Paper_numbers.ipynb ├── RPS24_scatter_2.ipynb ├── donor_acceptor_zscore.ipynb ├── gene_expression_vs_SZS.ipynb ├── ontology_heatmap.ipynb ├── output │ ├── donor_acceptor_zscore │ │ ├── HLCA4_P2_10x_with_postprocessing_lung.png │ │ ├── HLCA4_P2_10x_with_postprocessing_lung_CD47.png │ │ ├── HLCA4_P2_10x_with_postprocessing_lung_MYL6.png │ │ ├── HLCA4_P2_10x_with_postprocessing_lung_RPS24.png │ │ ├── HLCA4_P3_10x_with_postprocessing_lung.png │ │ ├── HLCA4_P3_10x_with_postprocessing_lung_CD47.png │ │ ├── HLCA4_P3_10x_with_postprocessing_lung_MYL6.png │ │ └── HLCA4_P3_10x_with_postprocessing_lung_RPS24.png │ ├── gene_expression_vs_SZS │ │ ├── numreads_v_SZS_CD47_HLCA4_P2_10x_with_postprocessing_lung.png │ │ ├── numreads_v_SZS_CD47_HLCA4_P3_10x_with_postprocessing_lung.png │ │ ├── numreads_v_SZS_HLCA4_P2_10x_with_postprocessing_lung.png │ │ ├── numreads_v_SZS_HLCA4_P3_10x_with_postprocessing_lung.png │ │ ├── numreads_v_SZS_MYL6_HLCA4_P2_10x_with_postprocessing_lung.png │ │ ├── numreads_v_SZS_MYL6_HLCA4_P3_10x_with_postprocessing_lung.png │ │ ├── numreads_v_SZS_RPS24_HLCA4_P2_10x_with_postprocessing_lung.png │ │ ├── numreads_v_SZS_RPS24_HLCA4_P3_10x_with_postprocessing_lung.png │ │ ├── numreads_v_corr_HLCA4_P2_10x_with_postprocessing_lung.png │ │ └── numreads_v_corr_HLCA4_P3_10x_with_postprocessing_lung.png │ ├── ontology_heatmap │ │ └── HLCA4_P2_10x_with_postprocessing_lung_HLCA4_P3_10x_with_postprocessing_lung_MYL6_RPS24_CD47.png │ └── supplemental_figures │ │ ├── P2_numreads_percell.pdf │ │ ├── P2_numreads_percell.png │ │ ├── P3_numreads_percell.pdf │ │ └── P3_numreads_percell.png ├── plot_FDRs.ipynb ├── plot_human_spermatogenesis.ipynb ├── plot_sims.ipynb ├── supplemental_figures.ipynb ├── supplemental_figures_revision.ipynb └── supplemental_figures_v2.ipynb ├── pipeline.png ├── scripts ├── SVD_subcol.py ├── SVD_zscore.py ├── annotate_SpliZsites.R ├── anova_factor.r ├── anova_zscore.r ├── donor_boxplots.py ├── dotplots_combdataset.py ├── final_FDRs_anova.py ├── final_FDRs_anova_factor.py ├── final_FDRs_mz.py ├── final_summary.py ├── find_SpliZsites.R ├── output │ └── .gitignore ├── parquet_to_tsv.py ├── perm_pvals.py ├── power_simulation.py ├── rewritten_subscripts │ └── run_sim.sh ├── rijk_zscore.py ├── significant_genes.py ├── submission_scripts │ ├── run_subcol.sh │ └── run_var.sh ├── submit_simulations.py ├── variance_adjusted_permutations.py └── variance_adjusted_permutations_bytiss.py ├── splice_summary.jpg ├── summary_test_compartment-tissue_100_S_0.1_z_0.0_b_5.tsv ├── test_pvals_compartment-tissue_100_S_0.1_z_0.0_b_5.tsv └── util_files └── .gitignore /.gitignore: -------------------------------------------------------------------------------- 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