# Analyze high-throughput sequencing of T and B cell receptors

## Documentation for package ‘LymphoSeq’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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