Analyze high-throughput sequencing of T and B cell receptors
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Documentation for package ‘LymphoSeq’ version 1.37.0
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 |