A toolkit for single-cell immune receptor profiling

---

Documentation for package ‘scRepertoire’ version 1.12.0

• 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