A toolkit for single-cell immune receptor profiling


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Documentation for package ‘scRepertoire’ version 2.2.1

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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 proportions / counts 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.
getContigDoublets Get Contig Doublets
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