| BLOSUM62 | BLOSUM62 matrix |
| CDR3ab | Datasets 'CDR3ab' and 'D1' with TCRalphabeta mock repertoires |
| class:clust_irr | clust_irr class |
| clustirr | Clustering of immune receptor repertoires (IRRs) |
| clust_irr | clust_irr class |
| clust_irr-class | clust_irr class |
| D1 | Datasets 'CDR3ab' and 'D1' with TCRalphabeta mock repertoires |
| dco | Model-based differential community occupancy (DCO) analysis |
| decode_communities | Decode graph communities |
| detect_communities | Graph-based community detection (GCD) |
| get_ag_summary | Estimate the number of antigen-specific T-cells in selected communities |
| get_beta_scatterplot | Compare community betas between pairs of repertoires |
| get_beta_violins | Visualize distribution of beta means in each repertoire as violin plots |
| get_clustirr_clust | clust_irr class |
| get_clustirr_clust-method | clust_irr class |
| get_clustirr_inputs | clust_irr class |
| get_clustirr_inputs-method | clust_irr class |
| get_honeycombs | Generate honycomb plot: visualize community occupancy of pairs of immune receptor repertoires |
| mcpas | CDR3 sequences and their matching epitopes obtained from McPAS-TCR |
| plot_graph | Plot ClustIRR graph |
| tcr3d | CDR3 sequences and their matching epitopes obtained from TCR3d |
| vdjdb | CDR3 sequences and their matching epitopes obtained from VDJdb |