Clustering of immune receptor repertoires

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Documentation for package ‘ClustIRR’ version 1.5.42

• 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
cluster_irr	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_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