# A toolkit for single-cell immune receptor profiling

## Documentation for package ‘scRepertoire’ version 1.10.0

- 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
clonalNetwork | Visualize clonal network along reduced dimensions
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 clonotypes
clonesizeDistribution | Hierarchical clustering of clonotypes on clonotype size and Jensen-Shannon divergence
clonotypeBias | Examine clonotype bias
clusterTCR | Clustering T cell receptors
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
combineTRUST4 | Combining the list of T or B cell Receptors from TRUST4 pipeline
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.
createHTOContigList | Generate a contig list from a multiplexed experiment
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.
loadContigs | Loading the contigs derived from single-cell sequencing
occupiedscRepertoire | Visualize the number of single cells with clonotype frequencies by cluster
quantContig | Quantify the unique clonotypes in the filtered contigs.
scatterClonotype | Scatter plot comparing the expansion of two samples
screp_example | A seurat object of 1000 single T cells derived from 3 clear cell renal carcinoma patients.
Startrac | The Startrac Class
Startrac-class | The Startrac Class
StartracDiversity | Diversity indices for single-cell RNA-seq
stripBarcode | Removing any additional prefixes to the barcodes of filtered contigs.
subsetContig | Subset the product of combineTCR() combineBCR() or expression2List()
vizGenes | Visualizing the distribution of gene usage