# A toolkit for single-cell immune receptor profiling

## Documentation for package ‘scRepertoire’ version 2.5.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addVariable | Adding Variables After combineTCR() or combineBCR()
alluvialClones | Alluvial Plotting for Single-Cell Object
annotateInvariant | Annotate invariant T cells (MAIT or iNKT) in single-cell TCR data
clonalAbundance | Plot the Relative Abundance of Clones
clonalBias | Calculate Clonal Bias Towards a Cluster or Compartment
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
clonalNetwork | Visualize Clonal Network in Dimensional Reductions
clonalOccupy | Plot cloneSize by Variable in Single-Cell Objects
clonalOverlap | Examining the clonal overlap between groups or samples
clonalOverlay | Visualize Distribution of Clonal Frequency
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
combineBCR | Combine B Cell Receptor Contig Data
combineExpression | Adding Clonal Information to Single-Cell Object
combineTCR | Combine T Cell Receptor Contig Data
contig_list | A List of Eight Single-cell TCR Sequencing Runs.
createHTOContigList | Deconvolute Contig Information from Multiplexed Experiments
exportClones | Export Clonal Data in Various Formats
getCirclize | Generate Data Frame to Plot Cord Diagram
getContigDoublets | Get Contig Doublets
highlightClones | Highlighting Specific Clones
loadContigs | Load Immune Receptor Sequencing Contigs
percentAA | Plot Relative Amino Acid Composition by Position
percentGenes | Summarizes and Visualizes Gene Usage
percentGeneUsage | Summarizes and Visualizes Gene Usage
percentKmer | Analyze K-mer Motif Composition
percentVJ | Summarizes and Visualizes Gene Usage
positionalEntropy | Examining the Diversity of Amino Acids by Position
positionalProperty | Plot Positional Physicochemical Property Analysis
quietBCRgenes | Remove TCR and BCR genes from variable gene results
quietBCRgenes.default | Remove TCR and BCR genes from variable gene results
quietBCRgenes.Seurat | Remove TCR and BCR genes from variable gene results
quietTCRgenes | Remove TCR and BCR genes from variable gene results
quietTCRgenes.default | Remove TCR and BCR genes from variable gene results
quietTCRgenes.Seurat | Remove TCR and BCR genes from variable gene results
quietVDJgenes | Remove TCR and BCR genes from variable gene results
scRep_example | A Seurat Object of 500 Single T cells,
StartracDiversity | Calculate Startrac-based Diversity Indices
subsetClones | Subset The Product of combineTCR() or combineBCR()
vizGenes | Summarizes and Visualizes Gene Usage