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-any)LymphoSeq_1.41.0.zip(r-4.6-any)LymphoSeq_1.41.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
LymphoSeq/json (API)

# 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

3.00 score 10 scripts 528 downloads 1 mentions 31 exports 103 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksERROR215
linux-develERROR316
source / vignettesERROR258
linux-releaseERROR343
macos-releaseERROR187
macos-oldrelERROR334
windows-develERROR145
windows-releaseERROR184
windows-oldrelERROR201
wasm-releaseOK175

Exports:alignSeqbhattacharyyaCoefficientbhattacharyyaMatrixchordDiagramVDJclonalityclonalRelatednesscloneTrackcommonSeqscommonSeqsBarcommonSeqsPlotcommonSeqsVenndifferentialAbundanceexportFastageneFreqlorenzCurvemergeFilespairwisePlotphyloTreeproductiveproductiveSeqreadImmunoSeqremoveSeqsearchPublishedsearchSeqseqMatrixsimilarityMatrixsimilarityScoretopFreqtopSeqstopSeqsPlotuniqueSeqs

Dependencies:apeaplotbase64encBiocGenericsBiostringsbslibcachemcirclizeclicolorspacecpp11crayondata.tabledigestdplyrevaluatefarverfastmapfastmatchfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgenericsggfunggiraphggplot2ggplotifyggtreeGlobalOptionsgluegridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetsigraphineqIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecycleLymphoSeqDBmagrittrMASSMatrixmemoisemimemsaMultipleAlignmentnlmepatchworkphangornpillarpkgconfigplyrpurrrquadprogR6rappdirsRColorBrewerRcppreshaperlangrmarkdownS4VectorsS7sassscalesSeqinfoshapestringdiststringistringrsystemfontstibbletidyrtidyselecttidytreetinytextreeioUpSetRutf8vctrsVennDiagramviridisLitewithrxfunXVectoryamlyulab.utils