# Clustering of immune receptor repertoires

## Documentation for package ‘ClustIRR’ version 1.8.0

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

## Help Pages

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_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_violin | 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_community_purity | Compute community purity with respect to a node feature
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