Package index • scRepertoire

Loading and Processing Contigs

Functions that load, combine, and process the single-cell contig information.

loadContigs(): Load Immune Receptor Sequencing Contigs
combineTCR(): Combine T Cell Receptor Contig Data
combineBCR(): Combine B Cell Receptor Contig Data
clonalBin(): Bin Clones by Frequency or Proportion
addVariable(): Adding Variables After combineTCR() or combineBCR()
subsetClones(): Subset The Product of combineTCR() or combineBCR()
exportClones(): Export Clonal Data in Various Formats
createHTOContigList(): Deconvolute Contig Information from Multiplexed Experiments
getContigDoublets() experimental: Get Contig Doublets
annotateInvariant(): Annotate invariant T cells (MAIT or iNKT) in single-cell TCR data

Functions for visualizing clonal data across samples and groups.

clonalAbundance(): Plot the Relative Abundance of Clones
clonalCompare(): Compare Clonal Abundance Across Variables
clonalDiversity(): Calculate Clonal Diversity
clonalHomeostasis(): Plot Clonal Homeostasis of the Repertoire
clonalLength(): Plot the Distribution of Sequence Lengths
clonalOverlap(): Examining the clonal overlap between groups or samples
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
percentGeneUsage() vizGenes() percentGenes() percentVJ(): Summarizes and Visualizes Gene Usage

Functions to summarize clonal sequences across the repertoire.

percentGeneUsage() vizGenes() percentGenes() percentVJ(): Summarizes and Visualizes Gene Usage
percentAA(): Plot Relative Amino Acid Composition by Position
percentKmer(): Analyze K-mer Motif Composition
positionalEntropy(): Examining the Diversity of Amino Acids by Position
positionalProperty(): Plot Positional Physicochemical Property Analysis

Functions for clustering clones by sequence similarity.

Functions to add or visualize clonal information along a single-cell object.

Helper functions for filtering gene signatures and converting data.

quietVDJgenes() quietTCRgenes() quietBCRgenes(): Remove TCR and BCR genes from variable gene results
expression2List() deprecated: DEPRECATED Take the meta data in seurat/SCE and place it into a list

Reference data for package functions.