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Compute TCR clonotype similarities in a repertoire with cluster_irr", "Step 2-3. Construct TCR repertoire graphs and join them into $J$", "Run steps 1-3 with clustirr", "Inspect the content of clust_irrs", "Inspect graphs with plot_graph", "You can evaluate $J$ with igraph", "Step 4. community detection with detect_communities", "Inspecting the outputs of detect_communities", "Qualitative similarity between community abundance vectors with get_honeycombs", "Quantitative similarity between community abundance vectors with get_cosine_similarity", "Summary of communities is provided in the detect_communities outputs", "Special functions: decoding communities with decode_community", "Step 5. differential community occupancy (DCO) with dco", "Step 6. 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