skills/bioskills/bio-alternative-splicing-single-cell-splicing/scripts/sc_splicing_brie2.py

• prepare_splicing_events · function · L11-L21 — def prepare_splicing_events(gtf_file, output_gff)
• count_splicing_reads · function · L24-L40 — def count_splicing_reads(bam_file, events_gff, output_dir, barcode_file, n_proc=15)
• run_brie2_inference · function · L43-L62 — def run_brie2_inference(count_h5ad, cell_features, output_h5ad)
• find_variable_splicing · function · L65-L91 — def find_variable_splicing(adata_splice, cell_type_col='cell_type', min_cells=50)
• pseudobulk_by_celltype · function · L94-L109 — def pseudobulk_by_celltype(adata, cell_type_col='cell_type')
• differential_splicing_pseudobulk · function · L112-L167 — def differential_splicing_pseudobulk(adata_splice, group1_cells, group2_cells)