skills/pydeseq2/scripts/run_deseq2_analysis.py

• load_and_validate_data · function · L34-L64 — def load_and_validate_data(counts_path, metadata_path, transpose_counts=True)
• filter_data · function · L67-L91 — def filter_data(counts_df, metadata, min_counts=10, condition_col=None)
• run_deseq2 · function · L94-L121 — def run_deseq2(counts_df, metadata, design, n_cpus=1)
• infer_shrink_coeff · function · L124-L134 — def infer_shrink_coeff(dds, contrast)
• run_statistical_tests · function · L137-L169 — def run_statistical_tests(dds, contrast, alpha=0.05, shrink_lfc=True, inference=None, shrink_coeff=None)
• save_results · function · L172-L215 — def save_results(ds, dds, output_dir, shrink_lfc=True)
• create_plots · function · L218-L281 — def create_plots(ds, output_dir)
• main · function · L284-L384 — def main()