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Single-Cell Objects", "clonalOverlay", "clonalNetwork", "Filtering Options for clonalNetwork()", "highlightClones", "clonalOccupy", "alluvialClones", "Basic Alluvial Plot", "Filtering to Top Clones", "Highlighting Specific Clones", "Visual Customization", "getCirclize and vizCirclize", "Quick Visualization with vizCirclize", "Manual Control with getCirclize", "Multi-Level Hierarchical Grouping", "Directional Flow", "Different Similarity Methods", "Subsetting and Proportion", "Quantifying Clonal Bias", "StartracDiversity", "Indices Output from StartracDiversity()", "Calculating a Single Index", "Pairwise Migration Analysis", "clonalBias", "Clustering by Edit Distance", "clonalCluster: Cluster by Sequence Similarity", "Core Concepts", "Understanding the threshold Parameter", "Demonstrating Basic Use", "Demonstrating Clustering with a Single-Cell Object", "Returning an igraph Object:", "Returning a Sparse Adjacency Matrix", "Using Both Chains", "Using Different Clustering Algorithms", 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