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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.