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LymphoSeq (version 1.0.2)

Analyze high-throughput sequencing of T and B cell receptors

Description

This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.

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Version

Version

1.0.2

License

Artistic-2.0

Maintainer

David Coffey

Last Published

February 15th, 2017

Functions in LymphoSeq (1.0.2)

searchSeq

Search for a sequence
removeSeq

Remove sequence
commonSeqs

Common sequences in two or more samples
chordDiagramVDJ

Chord diagram of VJ or DJ gene associations
readImmunoSeq

Read ImmunoSeq files
bhattacharyyaCoefficient

Bhattacharyya coefficient
commonSeqsVenn

Common sequences Venn diagram
similarityMatrix

Similarity score matrix
searchPublished

Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity
pairwisePlot

Pairwise comparison plot
mergeFiles

Merge files
clonality

Clonality
lorenzCurve

Lorenz curve
geneFreq

Gene frequencies
topSeqs

Top sequences
seqMatrix

Sequence matrix
productiveSeq

Productive sequences
topFreq

Top frequencies
similarityScore

Similarity score
uniqueSeqs

Unique sequences
commonSeqsPlot

Common sequences plot
productive

Productive sequences
cloneTrack

Clone tracking plot
bhattacharyyaMatrix

Bhattacharyya matrix
topSeqsPlot

Cumulative frequency bar plot of top sequences