$,FancyResult-method    Access FancyResult slots with '$'
FancyResult-class       FancyResult: S4 container for Fancy pipeline
                        output
bootstrap_networks      Bootstrap network inference
clean_sample_names      Clean sample names from TSV column headers
clr_normalize           CLR-normalise a count table
export_cytoscape        Export a fancy result for Cytoscape
fancy                   Run the full Fancy hybrid network inference
                        pipeline
fancy_tiny_clr          Tiny example CLR-transformed abundance table
fancy_tiny_counts       Tiny example count table
fancy_tiny_coverage     Tiny example covered-fraction table
fancy_tiny_metadata     Tiny example sample metadata
fancy_tiny_taxonomy     Tiny example GTDB taxonomy table
filter_mags             Filter MAGs by coverage and prevalence
find_optimal_k          Find optimal k for the kNN MI estimator
hybrid_score            Compute hybrid edge score
parse_count_tables      Parse per-sample TSV files into combined
                        MAG-by-sample matrices
parse_gtdb_taxonomy     Parse a GTDB-format taxonomy file
phyla_palette           Assign colours to phyla
plot,FancyResult,missing-method
                        Plot the hybrid score distribution of a
                        FancyResult
plot_k_elbow            Plot elbow curve for k selection
plot_network            Plot the co-abundance network
show,FancyResult-method
                        Display a FancyResult
threshold_edges         Threshold scored edges
