Package: LymphoSeq
Title: Analyze high-throughput sequencing of T and B cell receptors
Version: 1.40.0
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 cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:43:22 UTC
RemoteUrl: https://github.com/bioc/LymphoSeq
RemoteRef: RELEASE_3_23
RemoteSha: 0668ef1d058b75e99dcc05f825d04d33125670f6
Packaged: 2026-04-29 23:11:47 UTC; root
Built: R 4.6.0; ; 2026-04-29 23:14:16 UTC; windows
