as_path2path_matrix     Convert a SummarizedExperiment assay to a
                        path2path input matrix.
as_path2path_se         Convert a path2path map to a
                        SummarizedExperiment.
bh_populated            Benjamini-Hochberg over the populated (non-NA)
                        cells of a matrix.
build_null_pool         Whole-pipeline permutation null calibration.
calibrate_pvalues       One-call calibrated p-values for an existing
                        map.
dataset_tag             Dataset tag from a zscore_<tag>.csv[.gz]
                        filename.
demo_pathways           Synthetic demonstration pathway collection
demo_z                  Synthetic demonstration input matrix
jaccard_mask            Mask off-diagonal entries whose pathway pair
                        overlaps above 'tau'.
load_pathways           Load an MSigDB collection as a named list of
                        gene-symbol vectors.
order_by_activity       Pathway names ordered by number of significant
                        entries (descending).
path2path               Full two-stage GSEA pipeline: z matrix ->
                        pathway x pathway matrix.
pathway_jaccard         Pairwise Jaccard similarity of pathway gene
                        sets (dense crossproduct).
permute_input           Whole-matrix permutation: one global row and
                        one global column permutation.
plot_calibration        Route B diagnostics: null-pool tail versus the
                        fitted GPD.
plot_entry              GSEA-style enrichment plot for one map entry:
                        why is M[j, k] strong?
plot_map                Heatmap of a path2path map with significance
                        dots.
read_input_matrix       Read a z-score CSV (rows = perturbed gene
                        symbols in first column).
select_active           Pathways with at least 'min_sig' significant
                        entries, as regulators and as readouts.
stage1_nes              Stage 1: per-perturbation preranked GSEA.
stage2_matrix           Stage 2: per-pathway-column GSEA in the
                        perturbation universe.
write_result            Write pipeline outputs with dataset/collection
                        namespacing.
