Man pages for elulu3/LymphoSeqTest
Analyze high-throughput sequencing of T and B cell receptors
| aggreateSeq | Group productive sequences by repertoire |
| alignSeq | Align multiple sequences |
| bhattacharyyaCoefficient | Bhattacharyya coefficient |
| 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 repertoire_ids |
| commonSeqsBar | Common sequences bar plot |
| commonSeqsPlot | Common sequences plot |
| commonSeqsVenn | Common sequences Venn diagram |
| countKmer | Find kmers and its counts |
| differentialAbundance | Differential abundance analysis |
| exportFasta | Export sequences in fasta format |
| geneFreq | Gene frequencies |
| getGliphTable | Group productive sequences by repertoire |
| getLorenz | Calculate Lorenz curve |
| getRelatedness | Calculate relatedness |
| lorenzCurve | Lorenz curve |
| pairwisePlot | Pairwise comparison plot |
| percentSI | Percent similarity index |
| phyloTree | Create phylogenetic tree |
| plotAlignment | Visualize multiple sequence alignment of CDR3 sequences |
| plotRarefactionCurve | Plot rarefication and extrapolation curves for samples |
| plotTrack | Plot clone |
| plotTrackSingular | Highlight clones |
| productiveSeq | Productive sequences |
| readGliph | Read GLIPH files |
| readImmunoSeq | Read ImmunoSeq files |
| removeSeq | Remove sequence |
| runINext | Run iNEXT on repertoire_ids |
| scoringMatrix | Bhattacharyya, Similarity, Sorensen, or PSI matrix |
| searchDB | Search for T cell receptor beta CDR3 amino acid sequences... |
| searchIreceptor | Search for T cell receptor beta CDR3 amino acid sequences in... |
| searchPublished | Search for T cell receptor beta CDR3 amino acid sequences... |
| searchSeq | Search for a sequence |
| seqMatrix | Sequence matrix |
| similarityScore | Similarity score |
| sorensenIndex | Sorensen index |
| summarySeq | Get summary statistics for each repertoire_id in the analysis |
| topFreq | Top frequencies |
| topSeqs | Top sequences |
| topSeqsPlot | Cumulative frequency bar plot of top sequences |
| uniqueSeqs | Unique sequences |
