# A toolkit for single-cell immune receptor profiling

## Documentation for package ‘scRepertoire’ version 1.0.0

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

## Help Pages

abundanceContig | Demonstrate the relative abundance of clonotypes by group or sample.
addVariable | Adding variables after the combination of contigs.
alluvialClonotypes | Exploring interaction of clonotypes by seurat or SCE dynamics
clonalDiversity | Examine the clonal diversity of samples
clonalHomeostasis | Examining the clonal homeostasis
clonalOverlap | Examining the clonal overlap between groups or samples
clonalProportion | Examining the clonal space occupied by specific clonotypes
clonesizeDistribution | Hierarchical clustering of clonotypes on clonotype size and Jensen-Shannon divergence
combineBCR | Combining the list of B Cell Receptor contigs
combineExpression | Adding clonotype information to a seurat or SCE object
combineTCR | Combining the list of T Cell Receptor contigs
compareClonotypes | Demonstrate the difference in clonal proportion between clonotypes
contig_list | A data set of T cell contigs as a list outputed from the filter_contig_annotation files.
expression2List | Allows users to take the meta data in seurat/SCE and place it into a list that will work with all the functions
getCirclize | Generate data frame to be used with circlize R package to visualize clonotypes as a chord diagram.
highlightClonotypes | Highlighting specific clonotypes in Seurat
lengthContig | Demonstrate the distribution of lengths filtered contigs.
occupiedscRepertoire | Visualize the number of single cells with clonotype frequencies by cluster
quantContig | Quantify the unique clonotypes in the filtered contigs.
screp_example | A seurat object of 1000 single T cells derived from 3 clear cell renal carcinoma patients.
stripBarcode | Removing any additional prefixes to the barcodes of filtered contigs.
subsetContig | Subset the product of combineTCR() combineBCR() or expression2List()
vizVgenes | Visualizing the distribution of TCR V gene usage