Clustering of immune receptor repertoires


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Documentation for package ‘ClustIRR’ version 1.5.39

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BLOSUM62 BLOSUM62 matrix
CDR3ab Mock data set of complementarity determining region 3 (CDR3) sequences and variable (V) and joining (J) genes from the alpha and beta chains of 10,000 T cell receptors.
class:clust_irr clust_irr class
cluster_irr Clustering of immune receptor repertoires (IRRs)
clust_irr clust_irr class
clust_irr-class clust_irr class
dco Model-based differential community occupancy (DCO) analysis
detect_communities Graph-based community detection (GCD)
get_ag_summary Estimate the number of antigen-specific T-cells in selected communities
get_beta_violins Generate beta violin plot: visualize distribution of beta coefficient means for communities in immune receptor repertoires
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_graph Get 'igraph' object from 'clust_irr' object
get_honeycombs Generate honycomb plot: visualize community occupancy of pairs of immune receptor repertoires
get_joint_graph Create joint 'igraph' object from multiple 'clust_irr' objects
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