├── .DS_Store ├── .gitignore ├── LICENSE ├── README.md ├── configs ├── srr.yaml ├── srr_demo.yaml └── srr_star_demo.yaml ├── data ├── Demo_label.csv ├── Demo_results.csv ├── Demo_star_label.csv ├── junc_star │ ├── SRR7667417SJ.out.tab │ ├── SRR7667418SJ.out.tab │ ├── SRR7667419SJ.out.tab │ ├── SRR7667420SJ.out.tab │ ├── SRR7667424SJ.out.tab │ ├── SRR7667425SJ.out.tab │ ├── SRR7667427SJ.out.tab │ ├── SRR7667428SJ.out.tab │ ├── SRR7667429SJ.out.tab │ ├── SRR7667431SJ.out.tab │ ├── SRR7667434SJ.out.tab │ ├── SRR7667435SJ.out.tab │ ├── SRR7667442SJ.out.tab │ ├── SRR7667444SJ.out.tab │ ├── SRR7667446SJ.out.tab │ ├── SRR7667449SJ.out.tab │ ├── SRR7667455SJ.out.tab │ ├── SRR7667458SJ.out.tab │ ├── SRR7667463SJ.out.tab │ ├── SRR7667465SJ.out.tab │ ├── SRR7667470SJ.out.tab │ ├── SRR7667472SJ.out.tab │ ├── SRR7667474SJ.out.tab │ ├── SRR7667479SJ.out.tab │ ├── SRR7667481SJ.out.tab │ ├── SRR7667484SJ.out.tab │ ├── SRR7667485SJ.out.tab │ ├── SRR7667489SJ.out.tab │ ├── SRR7667490SJ.out.tab │ ├── SRR7667493SJ.out.tab │ ├── SRR7667496SJ.out.tab │ ├── SRR7667516SJ.out.tab │ ├── SRR7667518SJ.out.tab │ ├── SRR7667519SJ.out.tab │ ├── SRR7667530SJ.out.tab │ ├── SRR7667532SJ.out.tab │ └── SRR7667534SJ.out.tab └── junction │ ├── SRR7666346.junc │ ├── SRR7666347.junc │ ├── SRR7666348.junc │ ├── SRR7666351.junc │ ├── SRR7666352.junc │ ├── SRR7666354.junc │ ├── SRR7666355.junc │ ├── SRR7666357.junc │ ├── SRR7666358.junc │ ├── SRR7666480.junc │ ├── SRR7666481.junc │ ├── SRR7666482.junc │ ├── SRR7666483.junc │ ├── SRR7666484.junc │ ├── SRR7666485.junc │ ├── SRR7666487.junc │ ├── SRR7666488.junc │ ├── SRR7666490.junc │ ├── SRR7666494.junc │ ├── SRR7666495.junc │ ├── SRR7666497.junc │ ├── SRR7666498.junc │ ├── SRR7666500.junc │ ├── SRR7666581.junc │ ├── SRR7666583.junc │ ├── SRR7666586.junc │ ├── SRR7666588.junc │ ├── SRR7666589.junc │ ├── SRR7666591.junc │ ├── SRR7666592.junc │ ├── SRR7666595.junc │ ├── SRR7666596.junc │ ├── SRR7666599.junc │ └── SRR7666600.junc ├── leafcutter ├── bam2junc.sh ├── bed2junc.pl ├── filter_cs.py ├── leafcutter_cluster_regtools.py ├── prepare_phenotype_table.py └── sam2bed.pl ├── main.py ├── process_result_demo ├── cluster_result.csv ├── filtered_matrix_end.csv ├── filtered_matrix_start.csv ├── img │ ├── cluster.png │ ├── reduce.png │ ├── sample_hist.png │ └── site_hist.png ├── junc_mat.npy ├── junc_matrix.csv ├── normalized_matrix.csv ├── normalized_matrix.npy ├── samples.json ├── sites.json ├── sites_dict.json └── srr.yaml ├── requirements.txt └── scasl ├── __init__.py ├── __pycache__ ├── __init__.cpython-311.pyc ├── __init__.cpython-38.pyc ├── __init__.cpython-39.pyc ├── cluster.cpython-311.pyc ├── cluster.cpython-38.pyc ├── cluster.cpython-39.pyc ├── filter.cpython-311.pyc ├── filter.cpython-38.pyc ├── filter.cpython-39.pyc ├── normalize.cpython-311.pyc ├── normalize.cpython-38.pyc ├── normalize.cpython-39.pyc ├── process.cpython-311.pyc ├── process.cpython-38.pyc ├── process.cpython-39.pyc ├── splice.cpython-311.pyc ├── 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