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

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.

AuthorDavid Coffey <dcoffey@fredhutch.org>
Date of publicationNone
MaintainerDavid Coffey <dcoffey@fredhutch.org>
LicenseArtistic-2.0
Version1.2.0

View on Bioconductor

Functions

bhattacharyyaCoefficient Man page
bhattacharyyaMatrix Man page
chordDiagramVDJ Man page
clonality Man page
cloneTrack Man page
commonSeqs Man page
commonSeqsPlot Man page
commonSeqsVenn Man page
geneFreq Man page
lorenzCurve Man page
mergeFiles Man page
pairwisePlot Man page
productive Man page
productiveSeq Man page
readImmunoSeq Man page
removeSeq Man page
searchPublished Man page
searchSeq Man page
seqMatrix Man page
similarityMatrix Man page
similarityScore Man page
topFreq Man page
topSeqs Man page
topSeqsPlot Man page
uniqueSeqs Man page

Files

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

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