Man pages for shashidhar22/LymphoSeq2
Analyze high-throughput sequencing of T and B cell receptors
| alignSeq | Align multiple sequences |
| antigen_db | Antigen DB |
| bhattacharyyaCoefficient | Bhattacharyya coefficient |
| calculateCounts | Calculate k-mer counts |
| chordDiagramVDJ | Chord diagram of VJ or DJ gene associations |
| clonality | Clonality (summary statistics) |
| clonalRelatedness | Clonal relatedness |
| cloneTrack | Clone tracking line plot |
| collpase_chains | Read 10x Genomics data containing alpha and beta chains |
| commonSeqs | Common sequences in two or more repertoire_ids |
| commonSeqsBar | Common sequences bar plot |
| commonSeqsPlot | Common sequences scatter plot |
| commonSeqsVenn | Common sequences Venn diagram |
| countKmer | Find k-mers and its counts |
| differentialAbundance | Differential abundance analysis |
| exportFasta | Export sequences in fasta format |
| fisherFunction | Fisher test |
| geneFreq | Gene frequencies |
| getGliphTable | Group productive sequences by repertoire |
| getLorenz | Calculate Lorenz curve |
| getRelatedness | Calculate relatedness |
| iterativeSummary | Uncount, sample and iteratively calculate repertoire summary... |
| kmerPlot | Plot kmer distributions |
| lorenzCurve | Lorenz curve |
| LymphoSeq2-package | LymphoSeq2: Analyze high-throughput sequencing of T and B... |
| mostPrevalent | Selecting the alpha and beta chains |
| pairwiseNetwork | Pairwise comparison network graph |
| pairwisePlot | Pairwise comparison plot |
| percentSI | Percent similarity index |
| phyloTree | Create phylogenetic tree |
| plotAlignment | Visualize multiple sequence alignment of CDR3 sequences |
| plotRarefactionCurve | Plot rarefaction and extrapolation curves for samples |
| plotTrack | Clone tracking alluvial plot |
| plotTrackSingular | Highlight clones |
| prepDB | Create a antigen specific T-cells database |
| prevalenceTRB | Prevalence TRB |
| productiveSeq | Select productive sequences |
| publishedTRB | Published TRB |
| read10x | Read 10x Genomics files |
| readGliph | Read GLIPH files |
| readImmunoSeq | Read ImmunoSeq files |
| removeSeq | Remove sequence |
| runINext | Run iNEXT on repertoire_ids |
| sampledSummary | Sample repertoire |
| scoringMatrix | Bhattacharyya, Similarity, Sorensen, or PSI matrix |
| searchDB | Search for T cell receptor beta CDR3 amino acid sequences... |
| searchPublished | Search for T cell receptor beta CDR3 amino acid sequences... |
| searchSeq | Search for a sequence |
| selectChain | Select the most frequent chain |
| seqMatrix | Sequence matrix |
| similarityScore | Similarity score |
| sorensenIndex | Sorensen index |
| standardize10x | Standardize 10X data inputs |
| 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 |
| writeFasta | Write FASTA file |
