skills/bioskills/bio-genome-annotation-repeat-annotation/scripts/te_expression.py

• run_tetranscripts · function · L12-L31 — def run_tetranscripts(treatment_bams, control_bams, gene_gtf, te_gtf, output_prefix='te_analysis', stranded='no')
• parse_tetranscripts_output · function · L34-L46 — def parse_tetranscripts_output(count_table)
• te_family_summary · function · L49-L70 — def te_family_summary(te_counts)
• plot_te_expression · function · L73-L84 — def plot_te_expression(te_counts, top_n=30, output_file='te_expression.png')