attach_clonotypes       Attach Clonotypes to Existing Communities
BLOSUM62                BLOSUM62 matrix
clust_irr-class         clust_irr class
clustirr                Clustering of immune receptor repertoires
                        (IRRs)
D_CMV_FLU               Processed single-cell TCR and gene expression
                        dataset of antigen stimulated T cells
D1                      Synthetic dataset 'D1' with three TCRalphabeta
                        repertoires
D2                      Synthetic dataset 'D2' with six TCRalphabeta
                        repertoires
dco                     Model-based differential community occupancy
                        (DCO) analysis
decode_all_communities
                        Decode all graph communities
decode_community        Decode graph communities
detect_communities      Graph-based community detection (GCD)
get_ag_gene_hits        Annotate antigen gene hits in node summary
get_ag_species_hits     Annotate antigen species hits in node summary
get_beta_cprob_ag       Visualize cumulative probability of beta means
                        for antigen-specific communities
get_beta_violin_ag      Visualize distribution of beta means in each
                        repertoire as violin plots
get_cdr3_motifs         Generate CDR3 motif for communities
get_community_feature_purity
                        Compute community purity with respect to a node
                        feature
get_community_feature_stats
                        Compute descriptive statistics of a community
                        node feature
get_cosine_similarity   Compute and Visualize Cosine Similarity (CS)
get_honeycombs          Generate honycomb plot: visualize community
                        occupancy of pairs of immune receptor
                        repertoires
get_nrads               Compute Normalized Rank Abundance Distributions
                        (NRADs)
mcpas                   CDR3 sequences and their matching epitopes
                        obtained from McPAS-TCR
merge_clustirrs         Merge immune receptor repertoire similarity
                        graphs
plot_graph              Plot ClustIRR graph
save_interactive_graph
                        Save interactive ClustIRR graph
tcr3d                   CDR3 sequences and their matching epitopes
                        obtained from TCR3d
vdjdb                   CDR3 sequences and their matching epitopes
                        obtained from VDJdb
