A toolkit for single-cell immune receptor profiling


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Documentation for package ‘scRepertoire’ version 1.12.0

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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