Package: LymphoSeq 1.33.0

David Coffey

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.

Authors:David Coffey <[email protected]>

LymphoSeq_1.33.0.tar.gz
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LymphoSeq.pdf |LymphoSeq.html✨
LymphoSeq/json (API)
NEWS

# Install 'LymphoSeq' in R:
install.packages('LymphoSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:LymphoSeq-1.33.0(bioc 3.20)LymphoSeq-1.32.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

31 exports 0.82 score 91 dependencies 1 mentions

Last updated 2 months agofrom:fb0a3fc9be

Exports:alignSeqbhattacharyyaCoefficientbhattacharyyaMatrixchordDiagramVDJclonalityclonalRelatednesscloneTrackcommonSeqscommonSeqsBarcommonSeqsPlotcommonSeqsVenndifferentialAbundanceexportFastageneFreqlorenzCurvemergeFilespairwisePlotphyloTreeproductiveproductiveSeqreadImmunoSeqremoveSeqsearchPublishedsearchSeqseqMatrixsimilarityMatrixsimilarityScoretopFreqtopSeqstopSeqsPlotuniqueSeqs

Dependencies:apeaplotaskpassBiocGenericsBiostringscachemcirclizeclicolorspacecpp11crayoncurldata.tabledigestdplyrfansifarverfastmapfastmatchformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggfunggplot2ggplotifyggtreeGlobalOptionsgluegridExtragridGraphicsgtablehttrigraphineqIRangesisobandjsonlitelabelinglambda.rlatticelazyevallifecycleLymphoSeqDBmagrittrMASSMatrixmemoisemgcvmimemsamunsellnlmeopensslpatchworkphangornpillarpkgconfigplyrpurrrquadprogR6RColorBrewerRcppreshaperlangS4VectorsscalesshapestringdiststringistringrsystibbletidyrtidyselecttidytreetreeioUCSC.utilsUpSetRutf8vctrsVennDiagramviridisLitewithrXVectoryulab.utilszlibbioc

Analysis of high-throughput sequencing of T and B cell receptors with LymphoSeq

David G. Coffey, MD

Rendered fromLymphoSeq.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2017-04-14
Started: 2016-04-06