Package: scRepertoire 2.9.1

Introduction | Loading Libraries | Loading Data | What data to load into scRepertoire? | Demonstrating Manual Data Loading (10x Genomics) | Other alignment workflows | Supported Formats and Expected File Names | Multiplexed Experiment | Important Considerations for createHTOContigList() | Example Data in scRepertoire | Combining Contigs into Clones | combineBCR | How combineBCR() Groups Related Clones | Advanced: Grouping by Alignment | Filtering and Cleaning Data | Retaining Full-Length Sequences | Additional Processing | addVariable: Adding Variables for Plotting | subsetClones: Filter Out Clonal Information | exportClones: Save Clonal Data | clonalBin: Bin Clones by Frequency or Proportion | Basic Usage with Proportion | Using Frequency-Based Binning | Grouping by a Variable | annotateInvariant | Basic Clonal Visualizations | cloneCall: How to call clones. | clonalQuant: Quantifying Unique Clones | clonalAbundance: Distribution of Clones by Size | clonalLength: Distribution of Sequence Lengths | clonalCompare: Clonal Dynamics Between Categorical Variables | clonalScatter: Scatterplot of Two Variables | Visualizing Clonal Dynamics | clonalHomeostasis: Examining Clonal Space | clonalProportion: Examining Space Occupied by Ranks of Clones | Summarizing Repertoires | percentGeneUsage | vizGenes: Flexible Gene Usage Visualization | percentGenes: Quantifying Single Gene Usage | percentVJ: Quantifying V-J Gene Pairings | percentAA: Amino Acid Composition by Residue | positionalEntropy: Entropy across CDR3 Sequences | positionalProperty: Amino Acid Properties across CDR3 Sequence | percentKmer: Motif Quantification | Comparing Clonal Diversity and Overlap | clonalDiversity: Clonal Diversity Quantification | How clonalDiversity() Handles Downsampling and Bootstrapping | Available Diversity Metrics (metric) | clonalRarefaction: Sampling-based Extrapolation | Hill Numbers and Their Interpretation | plot.type Options | Rarefaction using Species Richness (q = 0) | Rarefaction using Shannon Diversity (q = 1) | clonalSizeDistribution: Modeling Clonal Composition | clonalOverlap: Exploring Sequence Overlap | method Parameters for clonalOverlap() | Combining Clones and Single-Cell Objects | Preprocessed Single-Cell Object | Note on Dimensional Reduction | Functions to Exclude VDJ Genes | combineExpression | Calculating cloneSize | Combining both TCR and BCR | Visualizations for 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 | Conclusion | Session Info