skills/bioskills/bio-atac-seq-differential-accessibility/scripts/diff_accessibility.R

• run_diff · function · L11-L76 — function(sample_sheet, output_prefix = 'diff_atac', normalize_mode = DBA_NORM_NATIVE, # Switch to DBA_NORM_LIB for global shift fdr_thr = 0.05, lfc_thr = 1, # Standard ENCODE-style thresholds min_overlap = 2, # Majority rule: peak in >= 2 reps fixed_width_summit = 250, # +/- 250 = 501 bp consensus (Corces 2018) use_sva = FALSE)