# A toolkit for single-cell immune receptor profiling

## Documentation for package ‘scRepertoire’ version 2.4.0

- 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 meta data
clonalAbundance | Demonstrate the relative abundance of clones by group or sample
clonalBias | Examine skew of clones towards a cluster or compartment
clonalCluster | Clustering adaptive receptor sequences by edit distance
clonalCompare | Demonstrate the difference in clonal proportions / counts between clones
clonalDiversity | Calculate the clonal diversity for samples or groupings
clonalHomeostasis | Examining the clonal homeostasis of the repertoire
clonalLength | Demonstrate the distribution of clonal length
clonalNetwork | Visualize clonal network along reduced dimensions
clonalOccupy | Visualize the number of single cells with cloneSizes by cluster
clonalOverlap | Examining the clonal overlap between groups or samples
clonalOverlay | Visualize distribution of clonal frequency overlaid on dimensional reduction plots
clonalProportion | Examining the clonal space occupied by specific clones
clonalQuant | Quantify the unique clones by group or sample
clonalRarefaction | Calculate rarefaction based on the abundance of clones
clonalScatter | Scatter plot comparing the clonal expansion of two samples
clonalSizeDistribution | Hierarchical clustering of clones using Gamma-GPD spliced threshold model
combineBCR | Combining the list of B cell receptor contigs into clones
combineExpression | Adding clone information to a single-cell object
combineTCR | Combining the list of T cell receptor contigs into clones
contig_list | A list of 8 single-cell T cell receptor sequences runs.
createHTOContigList | Generate a contig list from a multiplexed experiment
exportClones | Exporting clones
getCirclize | Generate data frame to be used with circlize R package to visualize clones as a chord diagram.
getContigDoublets | Get Contig Doublets
highlightClones | Highlighting specific clones in Seurat
loadContigs | Loading the contigs derived from single-cell sequencing
mini_contig_list | Processed subset of 'contig_list'
percentAA | Examining the relative amino acid composition by position
percentGenes | Examining the VDJ gene usage across clones
percentKmer | Examining the relative composition of kmer motifs in clones.
percentVJ | Quantifying the V and J gene usage across clones
positionalEntropy | Examining the diversity of amino acids by position
positionalProperty | Examining the mean property of amino acids by position
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 | Startrac-based diversity indices for single-cell RNA-seq
subsetClones | Subset the product of combineTCR() or combineBCR()
vizGenes | Visualizing the distribution of gene usage