cc_composition          Get peptides and peptide-to-protein mappings
                        for each connected component
cc_stats                Provide statistics on the CCs size
get_adj_matrix          Generate adjacency matrix
get_cc                  Generate graph and calculate its connected
                        components
peptide_stats           Calculate percentage of shared vs specific
                        peptides
plot_cc                 Plot peptide-to-protein mapping graph
read_inc_matrix         Read incidence matrix of proteomic
                        identifications
reduce_inc_matrix       Reduce size of incidence matrix for downstream
                        analyses
transcriptome_filter    Perform transcriptome-informed post-hoc
                        filtering
