Package: LymphoSeq 1.41.0

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_1.41.0.tar.gz
LymphoSeq_1.41.0.zip(r-4.7)LymphoSeq_1.41.0.zip(r-4.6)LymphoSeq_1.41.0.zip(r-4.5)
LymphoSeq_1.41.0.tgz(r-4.6-any)LymphoSeq_1.41.0.tgz(r-4.5-any)
LymphoSeq_1.41.0.tar.gz(r-4.7-any)LymphoSeq_1.41.0.tar.gz(r-4.6-any)
LymphoSeq_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
LymphoSeq/json (API)
NEWS

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

On BioConductor:LymphoSeq-1.41.0(bioc 3.24)LymphoSeq-1.40.0(bioc 3.23)

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

softwaretechnologysequencingtargetedresequencingalignmentmultiplesequencealignment

4.00 score 10 scripts 398 downloads 1 mentions 31 exports 102 dependencies

Last updated from:c95de6d869. Checks:1 ERROR, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR225
linux-devel-x86_64OK358
source / vignettesOK327
linux-release-x86_64OK368
macos-release-arm64OK255
macos-oldrel-arm64OK260
windows-develOK290
windows-releaseOK323
windows-oldrelOK292
wasm-releaseOK189

Exports:alignSeqbhattacharyyaCoefficientbhattacharyyaMatrixchordDiagramVDJclonalityclonalRelatednesscloneTrackcommonSeqscommonSeqsBarcommonSeqsPlotcommonSeqsVenndifferentialAbundanceexportFastageneFreqlorenzCurvemergeFilespairwisePlotphyloTreeproductiveproductiveSeqreadImmunoSeqremoveSeqsearchPublishedsearchSeqseqMatrixsimilarityMatrixsimilarityScoretopFreqtopSeqstopSeqsPlotuniqueSeqs

Dependencies:apeaplotbase64encBiocGenericsBiostringsbslibcachemcirclizeclicolorspacecpp11crayondata.tabledigestdplyrevaluatefarverfastmapfastmatchfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgenericsggfunggiraphggplot2ggplotifyggtreeGlobalOptionsgluegridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetsigraphineqIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecycleLymphoSeqDBmagrittrMASSMatrixmemoisemimemsanlmepatchworkphangornpillarpkgconfigplyrpurrrquadprogR6rappdirsRColorBrewerRcppreshaperlangrmarkdownS4VectorsS7sassscalesSeqinfoshapestringdiststringistringrsystemfontstibbletidyrtidyselecttidytreetinytextreeioUpSetRutf8vctrsVennDiagramviridisLitewithrxfunXVectoryamlyulab.utils

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

David G. Coffey, MD

Rendered fromLymphoSeq.Rmdusingknitr::rmarkdownon May 30 2026.

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