as_dfdr_tbl             Create a 'dfdr_tbl'
dfdr_bh_diagnostics     BH diagnostics at a headline alpha (threshold,
                        discoveries, boundary support)
dfdr_bh_elasticity      BH list elasticity (Jaccard) across alpha
                        values
dfdr_curve_stability    Stability curve across alpha values
dfdr_elasticity         Threshold elasticity (list stability to cutoff
                        perturbation)
dfdr_equal_chance_qbands
                        Equal-chance plausibility by q-value bands
dfdr_headline           Headline stability diagnostics at a given alpha
dfdr_local_tail         Local tail support near the cutoff
dfdr_p_calibration      P-value calibration diagnostic (ECDF vs
                        uniform; stratified)
dfdr_pep_decoy_sanity   Decoy PEP sanity checks
dfdr_pep_reliability    Posterior Error Probability (PEP) reliability
                        and internal PEP calibration error (IPE)
dfdr_pep_reliability_tdc
                        Target-focused PEP reliability using a
                        TDC-style error proxy
dfdr_pi0_storey         Storey pi_0(lambda) tail-uniformity diagnostic
dfdr_plot_bh_elasticity
                        Plot BH elasticity (Jaccard) vs alpha
dfdr_plot_cv            Plot 'CV_hat' versus 'alpha'
dfdr_plot_dalpha        Plot decoy support D_alpha versus 'alpha'
dfdr_plot_dwin          Plot local decoy support 'D_alpha_win' versus
                        'alpha'
dfdr_plot_elasticity    Plot threshold elasticity (Jaccard) versus
                        'alpha'
dfdr_plot_equal_chance
                        Plot equal-chance plausibility by q-value bands
dfdr_plot_fdrhat_pi0    Plot Storey-style estimated FDR curve: \hatpi_0
                        m t / R(t)
dfdr_plot_p_calibration
                        Plot p-value calibration (ECDF minus uniform)
dfdr_plot_p_calibration2
                        P-value calibration plot (cp4p-style), with
                        multiple pi0 reference curves
dfdr_plot_p_density_by_decoy
                        Plot (pseudo-)p-value density by decoy/target
dfdr_plot_pep_density_by_decoy
                        Plot PEP density by decoy/target
dfdr_plot_pep_reliability
                        Plot PEP reliability
dfdr_plot_pep_reliability_tdc
                        Plot target-focused PEP reliability (TDC-style)
dfdr_plot_pi0           Plot Storey pi_0(lambda) curve
dfdr_plot_scope_disagreement_matrix
                        Plot scope disagreement as a Jaccard overlap
                        heatmap
dfdr_plot_score_distributions
                        Plot target vs decoy score distributions
dfdr_render_report      Render a human-readable HTML report from
                        'dfdr_run_all' output
dfdr_run_all            Run a standard set of FDR QC diagnostics
dfdr_run_jaccard        Inter-run Jaccard overlap matrix at a fixed
                        threshold
dfdr_scope_disagreement
                        Scope disagreement between two lists
dfdr_summary_headline   Build a headline summary table (one row per
                        list)
dfdr_sumpep             Expected number of false targets among accepted
                        identifications
dfdr_write_manifest     Write a manifest file describing parameters,
                        list metadata, and warnings
dfdr_write_readme       Write a human-readable 'README.md' report
dfdr_write_report       Write diagnostic outputs to a folder
diann_global_minrunq    DIA-NN: global precursor list built by minimum
                        run-wise q across runs
diann_global_precursor
                        DIA-NN -> global precursor universe
                        (deduplicated by 'Precursor.Id')
diann_runxprecursor     DIA-NN -> run-by-precursor universe
                        (deduplicated within run)
flag_headline           Flag diagnostic values based on heuristic
                        thresholds
mokapot_competed_universe
                        Create a competed-winner universe from mokapot
                        PSM outputs
print.dfdr_tbl          Print a 'dfdr_tbl'
read_dfdr_maxquant_msms
                        Read MaxQuant 'msms.txt' into a 'dfdr_tbl'
                        (PSM-level; reconstructed TDC q-values)
read_dfdr_mzid          Read mzIdentML into a 'dfdr_tbl' (generic;
                        score-based TDC q-values)
read_diann_parquet      Read a DIA-NN 'report.parquet'
read_mokapot_psms       Read mokapot PSM text outputs (targets +
                        decoys) and combine
read_spectronaut        Read a Spectronaut TSV report
read_spectronaut_efficient
                        Read Spectronaut efficiently with column
                        selection
score_to_pvalue         Convert identification scores to p-values or
                        pseudo-p-values
spectronaut_runxprecursor
                        Spectronaut -> run-by-precursor universe
                        (deduplicated within run by 'EG.PrecursorId')
