# Clustering of Immune Receptor Repertoires

## Documentation for package ‘ClustIRR’ version 1.11.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

BLOSUM62 | BLOSUM62 matrix
CDR3ab | Datasets 'CDR3ab', 'D1' and 'D2' 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', 'D1' and 'D2' with TCRalphabeta mock repertoires
D2 | Datasets 'CDR3ab', 'D1' and 'D2' with TCRalphabeta mock 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_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_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
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