Package: LymphoSeq
Title: Analyze high-throughput sequencing of T and B cell receptors
Version: 1.39.0
Author: David Coffey <dcoffey@fredhutch.org>
Maintainer: David Coffey <dcoffey@fredhutch.org>
Description: 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.
Depends: R (>= 3.3), LymphoSeqDB
Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
        RColorBrewer, circlize, grid, utils, stats, ggtree, msa,
        Biostrings, phangorn, stringdist, UpSetR
License: Artistic-2.0
RoxygenNote: 6.0.1
Suggests: knitr, pheatmap, wordcloud, rmarkdown
VignetteBuilder: knitr
biocViews: Software, Technology, Sequencing, TargetedResequencing,
        Alignment, MultipleSequenceAlignment
NeedsCompilation: no
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libpng-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:31:49 UTC
RemoteUrl: https://github.com/bioc/LymphoSeq
RemoteRef: HEAD
RemoteSha: be99fc78ed3318b1a4ce66bec8adcb11acba6f7f
Packaged: 2026-01-20 07:59:02 UTC; root
Built: R 4.6.0; ; 2026-01-20 08:01:43 UTC; unix
