A toolkit for single-cell immune receptor profiling

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Documentation for package ‘scRepertoire’ version 2.1.0

• 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 proportion 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.
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
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