A toolkit for single-cell immune receptor profiling

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Documentation for package ‘scRepertoire’ version 2.5.3

• 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
annotateInvariant	Annotate invariant T cells (MAIT or iNKT) in single-cell TCR data
clonalAbundance	Plot the Relative Abundance of Clones
clonalBias	Calculate Clonal Bias Towards a Cluster or Compartment
clonalCluster	Cluster clones by sequence similarity
clonalCompare	Compare Clonal Abundance Across Variables
clonalDiversity	Calculate Clonal Diversity
clonalHomeostasis	Plot Clonal Homeostasis of the Repertoire
clonalLength	Plot the Distribution of Sequence Lengths
clonalNetwork	Visualize Clonal Network in Dimensional Reductions
clonalOccupy	Plot cloneSize by Variable in Single-Cell Objects
clonalOverlap	Examining the clonal overlap between groups or samples
clonalOverlay	Visualize Distribution of Clonal Frequency
clonalProportion	Plot the Clonal Space Occupied by Specific Clones
clonalQuant	Plot Number or Proportions of Clones
clonalRarefaction	Calculate rarefaction based on the abundance of clones
clonalScatter	Scatter Plot Comparing Clones Across Two Samples
clonalSizeDistribution	Plot powerTCR Clustering Based on Clonal Size
combineBCR	Combine B Cell Receptor Contig Data
combineExpression	Adding Clonal Information to Single-Cell Object
combineTCR	Combine T Cell Receptor Contig Data
contig_list	A List of Eight Single-cell TCR Sequencing Runs.
createHTOContigList	Deconvolute Contig Information from Multiplexed Experiments
exportClones	Export Clonal Data in Various Formats
getCirclize	Generate Data Frame to Plot Cord Diagram
getContigDoublets	Get Contig Doublets
highlightClones	Highlighting Specific Clones
loadContigs	Load Immune Receptor Sequencing Contigs
percentAA	Plot Relative Amino Acid Composition by Position
percentGenes	Summarizes and Visualizes Gene Usage
percentGeneUsage	Summarizes and Visualizes Gene Usage
percentKmer	Analyze K-mer Motif Composition
percentVJ	Summarizes and Visualizes Gene Usage
positionalEntropy	Examining the Diversity of Amino Acids by Position
positionalProperty	Plot Positional Physicochemical Property Analysis
quietBCRgenes	Remove TCR and BCR genes from variable gene results
quietBCRgenes.default	Remove TCR and BCR genes from variable gene results
quietBCRgenes.Seurat	Remove TCR and BCR genes from variable gene results
quietTCRgenes	Remove TCR and BCR genes from variable gene results
quietTCRgenes.default	Remove TCR and BCR genes from variable gene results
quietTCRgenes.Seurat	Remove TCR and BCR genes from variable gene results
quietVDJgenes	Remove TCR and BCR genes from variable gene results
scRep_example	A Seurat Object of 500 Single T cells,
StartracDiversity	Calculate Startrac-based Diversity Indices
subsetClones	Subset The Product of combineTCR() or combineBCR()
vizGenes	Summarizes and Visualizes Gene Usage