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✨
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 5 scripts 428 downloads 1 mentions 31 exports 103 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksERROR254
linux-devel-x86_64ERROR323
source / vignettesERROR280
linux-release-x86_64ERROR315
macos-release-arm64ERROR161
macos-oldrel-arm64ERROR247
windows-develERROR252
windows-releaseERROR255
windows-oldrelERROR247
wasm-releaseOK234

Exports:alignSeqbhattacharyyaCoefficientbhattacharyyaMatrixchordDiagramVDJclonalityclonalRelatednesscloneTrackcommonSeqscommonSeqsBarcommonSeqsPlotcommonSeqsVenndifferentialAbundanceexportFastageneFreqlorenzCurvemergeFilespairwisePlotphyloTreeproductiveproductiveSeqreadImmunoSeqremoveSeqsearchPublishedsearchSeqseqMatrixsimilarityMatrixsimilarityScoretopFreqtopSeqstopSeqsPlotuniqueSeqs

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