Package index
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alignSeq() - Align multiple sequences
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antigen_db - Antigen DB
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bhattacharyyaCoefficient() - Bhattacharyya coefficient
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calculateCounts() - Calculate k-mer counts
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chordDiagramVDJ() - Chord diagram of VJ or DJ gene associations
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clonalRelatedness() - Clonal relatedness
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clonality() - Calculate repertoire diversity metrics
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cloneTrack() - Clone tracking line plot
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collapse_chains() - Read 10x Genomics data containing alpha and beta chains
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commonSeqs() - Common sequences in two or more repertoire_ids
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commonSeqsBar() - Common sequences bar plot
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commonSeqsPlot() - Common sequences scatter plot
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commonSeqsVenn() - Common sequences Venn diagram
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countKmer() - Find k-mers and its counts
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detect_10x_format() - Detect 10x file format
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differentialAbundance() - Differential abundance analysis
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exportFasta() - Export sequences in fasta format
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fisherFunction() - Fisher test
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geneFreq() - Gene frequencies
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geneWordCloud() - Create word cloud visualization of gene frequencies
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getGliphTable() - Group productive sequences by repertoire
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getLorenz() - Calculate Lorenz curve
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getPrevalenceTRB() - Prevalence TRB
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getRelatedness() - Calculate relatedness
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iterativeSummary() - Calculate rarefied diversity metrics through repeated subsampling
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kmerPlot() - Plot kmer distributions
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lorenzCurve() - Lorenz curve
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merge_chains() - Merge paired TCR chains by cell
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mostPrevalent() - Selecting the alpha and beta chains
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pairwiseNetwork() - Pairwise comparison network graph
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pairwisePlot() - Pairwise comparison plot
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percentSI() - Percent similarity index
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phyloTree() - Create phylogenetic tree
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plotAlignment() - Visualize multiple sequence alignment of CDR3 sequences
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plotRarefactionCurve() - Plot rarefaction and extrapolation curves for samples
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plotTrack() - Clone tracking alluvial plot
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plotTrackSingular()highlightPlot() - Highlight clones
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prepDB() - Create a antigen specific T-cells database
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productiveSeq() - Select productive sequences
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publishedTRB - Published TRB
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read10x() - Import 10x Genomics single-cell VDJ data
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readGliph() - Read GLIPH files
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readImmunoSeq() - Read ImmunoSeq files
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read_airr_format() - Read AIRR-formatted 10x file
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read_contig_annotations() - Read contig_annotations format
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removeSeq() - Remove sequence
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runINext() - Generate rarefaction curves for diversity estimation
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sampledSummary() - Sample repertoire to fixed depth and calculate diversity
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scoringMatrix() - Bhattacharyya, Similarity, Sorensen, or PSI matrix
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searchDB() - Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity from IEDB, VdjDB and McPASDb
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searchPublished() - Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity
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searchSeq()findSeq() - Search for a sequence
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selectChain() - Select the most frequent chain
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seqMatrix() - Sequence matrix
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similarityScore() - Similarity score
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sorensenIndex() - Sorensen index
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standardize10x() - Standardize 10X data inputs
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summarySeq() - Get summary statistics for each repertoire_id in the analysis
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topFreq() - Top frequencies
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topSeqs() - Top sequences
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topSeqsPlot() - Cumulative frequency bar plot of top sequences
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uniqueSeqs() - Unique sequences
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writeFasta() - Write FASTA file