Package: LymphoSeq 1.40.0

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_1.40.0.tar.gz
LymphoSeq_1.40.0.zip(r-4.7-any)LymphoSeq_1.40.0.zip(r-4.6-any)LymphoSeq_1.40.0.zip(r-4.5-any)
LymphoSeq_1.40.0.tgz(r-4.6-any)LymphoSeq_1.40.0.tgz(r-4.5-any)
LymphoSeq_1.40.0.tar.gz(r-4.7-any)LymphoSeq_1.40.0.tar.gz(r-4.6-any)
LymphoSeq_1.40.0.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-release.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.

software technology sequencing targetedresequencing alignment multiplesequencealignment

4.00 score 10 scripts 528 downloads 1 mentions 31 exports 102 dependencies

Last updated from:0668ef1d05 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	244
linux-devel	OK	417
source / vignettes	OK	360
linux-release	OK	412
macos-release	OK	288
macos-oldrel	OK	258
windows-devel	OK	264
windows-release	OK	251
windows-oldrel	OK	242
wasm-release	OK	191

Exports:alignSeq bhattacharyyaCoefficient bhattacharyyaMatrix chordDiagramVDJ clonality clonalRelatedness cloneTrack commonSeqs commonSeqsBar commonSeqsPlot commonSeqsVenn differentialAbundance exportFasta geneFreq lorenzCurve mergeFiles pairwisePlot phyloTree productive productiveSeq readImmunoSeq removeSeq searchPublished searchSeq seqMatrix similarityMatrix similarityScore topFreq topSeqs topSeqsPlot uniqueSeqs

Dependencies:ape aplot base64enc BiocGenerics Biostrings bslib cachem circlize cli colorspace cpp11 crayon data.table digest dplyr evaluate farver fastmap fastmatch fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools generics ggfun ggiraph ggplot2 ggplotify ggtree GlobalOptions glue gridExtra gridGraphics gtable highr htmltools htmlwidgets igraph ineq IRanges isoband jquerylib jsonlite knitr labeling lambda.r lattice lazyeval lifecycle LymphoSeqDB magrittr MASS Matrix memoise mime msa nlme patchwork phangorn pillar pkgconfig plyr purrr quadprog R6 rappdirs RColorBrewer Rcpp reshape rlang rmarkdown S4Vectors S7 sass scales Seqinfo shape stringdist stringi stringr systemfonts tibble tidyr tidyselect tidytree tinytex treeio UpSetR utf8 vctrs VennDiagram viridisLite withr xfun XVector yaml yulab.utils

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

Rendered fromLymphoSeq.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Align mutliple sequences	alignSeq
Bhattacharyya coefficient	bhattacharyyaCoefficient
Bhattacharyya matrix	bhattacharyyaMatrix
Chord diagram of VJ or DJ gene associations	chordDiagramVDJ
Clonality	clonality
Clonal relatedness	clonalRelatedness
Clone tracking plot	cloneTrack
Common sequences in two or more samples	commonSeqs
Common sequences bar plot	commonSeqsBar
Common sequences plot	commonSeqsPlot
Common sequences Venn diagram	commonSeqsVenn
Differential abundance analysis	differentialAbundance
Export sequences in fasta format	exportFasta
Gene frequencies	geneFreq
Lorenz curve	lorenzCurve
Merge files	mergeFiles
Pairwise comparison plot	pairwisePlot
Create phylogenetic tree	phyloTree
Productive sequences	productive
Productive sequences	productiveSeq
Read ImmunoSeq files	readImmunoSeq
Remove sequence	removeSeq
Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity	searchPublished
Search for a sequence	searchSeq
Sequence matrix	seqMatrix
Similarity score matrix	similarityMatrix
Similarity score	similarityScore
Top frequencies	topFreq
Top sequences	topSeqs
Cumulative frequency bar plot of top sequences	topSeqsPlot
Unique sequences	uniqueSeqs