Analyze high-throughput sequencing of T and B cell receptors


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Documentation for package ‘LymphoSeq’ version 1.10.0

Help Pages

alignSeq Align mutliple sequences
bhattacharyyaCoefficient Bhattacharyya coefficient
bhattacharyyaMatrix Bhattacharyya matrix
chordDiagramVDJ Chord diagram of VJ or DJ gene associations
clonality Clonality
clonalRelatedness Clonal relatedness
cloneTrack Clone tracking plot
commonSeqs Common sequences in two or more samples
commonSeqsBar Common sequences bar plot
commonSeqsPlot Common sequences plot
commonSeqsVenn Common sequences Venn diagram
differentialAbundance Differential abundance analysis
exportFasta Export sequences in fasta format
geneFreq Gene frequencies
lorenzCurve Lorenz curve
mergeFiles Merge files
pairwisePlot Pairwise comparison plot
phyloTree Create phylogenetic tree
productive Productive sequences
productiveSeq Productive sequences
readImmunoSeq Read ImmunoSeq files
removeSeq Remove sequence
searchPublished Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity
searchSeq Search for a sequence
seqMatrix Sequence matrix
similarityMatrix Similarity score matrix
similarityScore Similarity score
topFreq Top frequencies
topSeqs Top sequences
topSeqsPlot Cumulative frequency bar plot of top sequences
uniqueSeqs Unique sequences