Loading and Processing ContigsFunctions that load, combine, and process the single-cell contig information. |
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Adding variables after combineTCR() or combineBCR() |
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Combining the list of B cell receptor contigs into clones |
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Combining the list of T cell receptor contigs into clones |
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Generate a contig list from a multiplexed experiment |
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Get Contig Doublets |
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Exporting clones |
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Loading the contigs derived from single-cell sequencing |
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Subset the product of combineTCR() or combineBCR() |
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Visualizing ClonesFunctions plotting clonal data. |
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Demonstrate the relative abundance of clones by group or sample |
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Clustering adaptive receptor sequences by edit distance |
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Demonstrate the difference in clonal proportions / counts between clones |
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Calculate the clonal diversity for samples or groupings |
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Examining the clonal homeostasis of the repertoire |
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Demonstrate the distribution of clonal length |
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Examining the clonal overlap between groups or samples |
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Examining the clonal space occupied by specific clones |
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Quantify the unique clones by group or sample |
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Calculate rarefaction based on the abundance of clones |
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Scatter plot comparing the clonal expansion of two samples |
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Hierarchical clustering of clones using Gamma-GPD spliced threshold model |
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Visualizing the distribution of gene usage |
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Summarizing RepertoireFunctions to summarize clonal sequences across the repertoire. |
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Examining the relative amino acid composition by position |
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Examining the diversity of amino acids by position |
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Examining the mean property of amino acids by position |
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Examining the VDJ gene usage across clones |
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Examining the relative composition of kmer motifs in clones. |
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Quantifying the V and J gene usage across clones |
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Single-Cell Object Processing and VisualizationsFunctions to add or visualize clonal information along a single-cell object. |
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Alluvial plotting for single-cell object meta data |
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Examine skew of clones towards a cluster or compartment |
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Visualize clonal network along reduced dimensions |
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Visualize the number of single cells with cloneSizes by cluster |
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Visualize distribution of clonal frequency overlaid on dimensional reduction plots |
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Adding clone information to a single-cell object |
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Generate data frame to be used with circlize R package to visualize clones as a chord diagram. |
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Highlighting specific clones in Seurat |
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Startrac-based diversity indices for single-cell RNA-seq |
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DataReference data for package functions. |
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A list of 8 single-cell T cell receptor sequences runs. |
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Processed subset of |
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A Seurat object of 500 single T cells, |