Package: LymphoSeq 1.35.0

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_1.35.0.tar.gz
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LymphoSeq_1.35.0.tgz(r-4.4-any)LymphoSeq_1.35.0.tgz(r-4.3-any)
LymphoSeq_1.35.0.tar.gz(r-4.5-noble)LymphoSeq_1.35.0.tar.gz(r-4.4-noble)
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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-1.35.0(bioc 3.21)LymphoSeq-1.34.0(bioc 3.20)

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

softwaretechnologysequencingtargetedresequencingalignmentmultiplesequencealignment

4.00 score 4 scripts 214 downloads 1 mentions 31 exports 88 dependencies

Last updated 2 months agofrom:1b80972e22. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:alignSeqbhattacharyyaCoefficientbhattacharyyaMatrixchordDiagramVDJclonalityclonalRelatednesscloneTrackcommonSeqscommonSeqsBarcommonSeqsPlotcommonSeqsVenndifferentialAbundanceexportFastageneFreqlorenzCurvemergeFilespairwisePlotphyloTreeproductiveproductiveSeqreadImmunoSeqremoveSeqsearchPublishedsearchSeqseqMatrixsimilarityMatrixsimilarityScoretopFreqtopSeqstopSeqsPlotuniqueSeqs

Dependencies:apeaplotaskpassBiocGenericsBiostringscirclizeclicolorspacecpp11crayoncurldata.tabledigestdplyrfansifarverfastmatchformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggfunggplot2ggplotifyggtreeGlobalOptionsgluegridExtragridGraphicsgtablehttrigraphineqIRangesisobandjsonlitelabelinglambda.rlatticelazyevallifecycleLymphoSeqDBmagrittrMASSMatrixmgcvmimemsamunsellnlmeopensslpatchworkphangornpillarpkgconfigplyrpurrrquadprogR6RColorBrewerRcppreshaperlangS4VectorsscalesshapestringdiststringistringrsystibbletidyrtidyselecttidytreetreeioUCSC.utilsUpSetRutf8vctrsVennDiagramviridisLitewithrXVectoryulab.utilszlibbioc

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

David G. Coffey, MD

Rendered fromLymphoSeq.Rmdusingknitr::rmarkdownon Nov 29 2024.

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