skills/bioskills/bio-liquid-biopsy-methylation-based-detection/scripts/cfdna_methylation.py

• choose_trimming · function · L14-L16 — def choose_trimming(reference, bam, prefix)
• extract_methylation · function · L19-L32 — def extract_methylation(reference, bam, prefix, min_depth=1, trim=None)
• deconvolve_tissue · function · L35-L41 — def deconvolve_tissue(sample_beta, atlas)
• region_dmrs · function · L44-L60 — def region_dmrs(cancer, normal, region_col='region', min_samples=3)
• haplotype_concordance_score · function · L63-L76 — def haplotype_concordance_score(read_states, background_p=0.05)