Package index • scRepertoire

Loading and Processing Contigs Functions that load, combine, and process the single-cell contig information.
`addVariable()`	Adding Variables After combineTCR() or combineBCR()
`combineBCR()`	Combine B Cell Receptor Contig Data
`combineTCR()`	Combine T Cell Receptor Contig Data
`createHTOContigList()`	Deconvolute Contig Information from Multiplexed Experiments
`getContigDoublets()`	Get Contig Doublets
`exportClones()`	Export Clonal Data in Various Formats
`loadContigs()`	Load Immune Receptor Sequencing Contigs
`subsetClones()`	Subset The Product of combineTCR() or combineBCR()
`annotateInvariant()`	Annotate invariant T cells (MAIT or iNKT) in single-cell TCR data
Visualizing Clones Functions plotting clonal data.
`clonalAbundance()`	Plot the Relative Abundance of Clones
`clonalCluster()`	Cluster clones by sequence similarity
`clonalCompare()`	Compare Clonal Abundance Across Variables
`clonalDiversity()`	Calculate Clonal Diversity
`clonalHomeostasis()`	Plot Clonal Homeostasis of the Repertoire
`clonalLength()`	Plot the Distribution of Sequence Lengths
`clonalOverlap()`	Examining the clonal overlap between groups or samples
`clonalProportion()`	Plot the Clonal Space Occupied by Specific Clones
`clonalQuant()`	Plot Number or Proportions of Clones
`clonalRarefaction()`	Calculate rarefaction based on the abundance of clones
`clonalScatter()`	Scatter Plot Comparing Clones Across Two Samples
`clonalSizeDistribution()`	Plot powerTCR Clustering Based on Clonal Size
`percentGeneUsage()` `vizGenes()` `percentGenes()` `percentVJ()`	Summarizes and Visualizes Gene Usage
Summarizing Repertoire Functions to summarize clonal sequences across the repertoire.
`percentAA()`	Plot Relative Amino Acid Composition by Position
`positionalEntropy()`	Examining the Diversity of Amino Acids by Position
`positionalProperty()`	Plot Positional Physicochemical Property Analysis
`percentGeneUsage()` `vizGenes()` `percentGenes()` `percentVJ()`	Summarizes and Visualizes Gene Usage
`percentKmer()`	Analyze K-mer Motif Composition
Single-Cell Object Processing and Visualizations Functions to add or visualize clonal information along a single-cell object.
`alluvialClones()`	Alluvial Plotting for Single-Cell Object
`clonalBias()`	Calculate Clonal Bias Towards a Cluster or Compartment
`clonalNetwork()`	Visualize Clonal Network in Dimensional Reductions
`clonalOccupy()`	Plot cloneSize by Variable in Single-Cell Objects
`clonalOverlay()`	Visualize Distribution of Clonal Frequency
`combineExpression()`	Adding Clonal Information to Single-Cell Object
`getCirclize()`	Generate Data Frame to Plot Cord Diagram
`highlightClones()`	Highlighting Specific Clones
`quietVDJgenes()` `quietTCRgenes()` `quietBCRgenes()`	Remove TCR and BCR genes from variable gene results
`StartracDiversity()`	Calculate Startrac-based Diversity Indices
Data Reference data for package functions.
`contig_list`	A List of Eight Single-cell TCR Sequencing Runs.
`scRep_example`	A Seurat Object of 500 Single T cells,

Reference

Loading and Processing Contigs

Visualizing Clones

Summarizing Repertoire

Single-Cell Object Processing and Visualizations

Data