LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

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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.

Author
David Coffey <dcoffey@fredhutch.org>
Date of publication
None
Maintainer
David Coffey <dcoffey@fredhutch.org>
License
Artistic-2.0
Version
1.2.0

View on Bioconductor

Man pages

bhattacharyyaCoefficient
Bhattacharyya coefficient
bhattacharyyaMatrix
Bhattacharyya matrix
chordDiagramVDJ
Chord diagram of VJ or DJ gene associations
clonality
Clonality
cloneTrack
Clone tracking plot
commonSeqs
Common sequences in two or more samples
commonSeqsPlot
Common sequences plot
commonSeqsVenn
Common sequences Venn diagram
geneFreq
Gene frequencies
lorenzCurve
Lorenz curve
mergeFiles
Merge files
pairwisePlot
Pairwise comparison plot
productive
Productive sequences
productiveSeq
Productive sequences
readImmunoSeq
Read ImmunoSeq files
removeSeq
Remove sequence
searchPublished
Search for T cell receptor beta CDR3 amino acid sequences...
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

Files in this package

LymphoSeq/DESCRIPTION
LymphoSeq/NAMESPACE
LymphoSeq/R
LymphoSeq/R/bhattacharyyaCoefficient.R
LymphoSeq/R/bhattacharyyaMatrix.R
LymphoSeq/R/chordDiagramVDJ.R
LymphoSeq/R/clonality.R
LymphoSeq/R/cloneTrack.R
LymphoSeq/R/commonSeqs.R
LymphoSeq/R/commonSeqsPlot.R
LymphoSeq/R/commonSeqsVenn.R
LymphoSeq/R/geneFreq.R
LymphoSeq/R/lorenzCurve.R
LymphoSeq/R/mergeFiles.R
LymphoSeq/R/pairwisePlot.R
LymphoSeq/R/productive.R
LymphoSeq/R/productiveSeq.R
LymphoSeq/R/readImmunoSeq.R
LymphoSeq/R/removeSeq.R
LymphoSeq/R/searchPublished.R
LymphoSeq/R/searchSeq.R
LymphoSeq/R/seqMatrix.R
LymphoSeq/R/similarityMatrix.R
LymphoSeq/R/similarityScore.R
LymphoSeq/R/topFreq.R
LymphoSeq/R/topSeqs.R
LymphoSeq/R/topSeqsPlot.R
LymphoSeq/R/uniqueSeqs.R
LymphoSeq/build
LymphoSeq/build/vignette.rds
LymphoSeq/inst
LymphoSeq/inst/NEWS
LymphoSeq/inst/doc
LymphoSeq/inst/doc/LymphoSeq.R
LymphoSeq/inst/doc/LymphoSeq.Rmd
LymphoSeq/inst/doc/LymphoSeq.pdf
LymphoSeq/inst/extdata
LymphoSeq/inst/extdata/TCRB_sequencing
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day0_Unsorted.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day1320_CD8_CMV.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day1320_Unsorted.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day32_Unsorted.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day369_CD8_CMV.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day369_Unsorted.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day83_CD8_CMV.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day83_Unsorted.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day949_CD4.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day949_CD8.tsv
LymphoSeq/inst/extdata/TCRB_sequencing/TCRB_Day949_Unsorted.tsv
LymphoSeq/inst/extdata/metadata.csv
LymphoSeq/man
LymphoSeq/man/bhattacharyyaCoefficient.Rd
LymphoSeq/man/bhattacharyyaMatrix.Rd
LymphoSeq/man/chordDiagramVDJ.Rd
LymphoSeq/man/clonality.Rd
LymphoSeq/man/cloneTrack.Rd
LymphoSeq/man/commonSeqs.Rd
LymphoSeq/man/commonSeqsPlot.Rd
LymphoSeq/man/commonSeqsVenn.Rd
LymphoSeq/man/geneFreq.Rd
LymphoSeq/man/lorenzCurve.Rd
LymphoSeq/man/mergeFiles.Rd
LymphoSeq/man/pairwisePlot.Rd
LymphoSeq/man/productive.Rd
LymphoSeq/man/productiveSeq.Rd
LymphoSeq/man/readImmunoSeq.Rd
LymphoSeq/man/removeSeq.Rd
LymphoSeq/man/searchPublished.Rd
LymphoSeq/man/searchSeq.Rd
LymphoSeq/man/seqMatrix.Rd
LymphoSeq/man/similarityMatrix.Rd
LymphoSeq/man/similarityScore.Rd
LymphoSeq/man/topFreq.Rd
LymphoSeq/man/topSeqs.Rd
LymphoSeq/man/topSeqsPlot.Rd
LymphoSeq/man/uniqueSeqs.Rd
LymphoSeq/vignettes
LymphoSeq/vignettes/LymphoSeq.Rmd