{
  "_id": "6aeaf6ec9ceaa78f2009ea3f",
  "Package": "LymphoSeq",
  "Title": "Analyze high-throughput sequencing of T and B cell receptors",
  "Version": "1.41.0",
  "Author": "David Coffey <dcoffey@fredhutch.org>",
  "Maintainer": "David Coffey <dcoffey@fredhutch.org>",
  "Description": "This R package analyzes high-throughput sequencing of T\nand B cell receptor complementarity determining region 3 (CDR3)\nsequences generated by Adaptive Biotechnologies' ImmunoSEQ\nassay.  Its input comes from tab-separated value (.tsv) files\nexported from the ImmunoSEQ analyzer.",
  "License": "Artistic-2.0",
  "RoxygenNote": "6.0.1",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Technology, Sequencing, TargetedResequencing,\nAlignment, MultipleSequenceAlignment",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:22 UTC",
  "RemoteUrl": "https://github.com/bioc/LymphoSeq",
  "RemoteRef": "HEAD",
  "RemoteSha": "c95de6d86903ff4c15fe7900606d6f59ab394102",
  "Packaged": {
    "Date": "2026-11-04 09:05:09 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "LymphoSeq_1.41.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/bd8d6d34e3a9e2369ec3757cc66c6a763ed26d137845a0725b8913486d8cd279",
  "_filesize": 897293,
  "_sha256": "bd8d6d34e3a9e2369ec3757cc66c6a763ed26d137845a0725b8913486d8cd279",
  "_expires": "2027-02-12T09:12:10.000Z",
  "_created": "2026-11-04T09:05:09.000Z",
  "_published": "2026-11-04T09:12:12.301Z",
  "_upstream": "https://github.com/bioc/LymphoSeq",
  "_status": "failure",
  "_maintainer": {
    "name": "David Coffey",
    "email": "dcoffey@fredhutch.org"
  },
  "_jobs": [
    {
      "job": 126488467908,
      "time": 214,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13309542235"
    },
    {
      "job": 126488467867,
      "time": 366,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "13308483978"
    },
    {
      "job": 126488467841,
      "time": 309,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13309398126"
    },
    {
      "job": 126488467992,
      "time": 251,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "13308783565"
    },
    {
      "job": 126488468007,
      "time": 274,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13309238557"
    },
    {
      "job": 126486186686,
      "time": 301,
      "config": "source",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13308557911"
    },
    {
      "job": 126488468003,
      "time": 169,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13308354654"
    },
    {
      "job": 126488467905,
      "time": 222,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "13309028847"
    },
    {
      "job": 126488468032,
      "time": 229,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "13308533656"
    },
    {
      "job": 126488468014,
      "time": 210,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13309153478"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714",
  "_commit": {
    "id": "c95de6d86903ff4c15fe7900606d6f59ab394102",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380202
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "LymphoSeqDB",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "reshape",
      "role": "Imports"
    },
    {
      "package": "VennDiagram",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ineq",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "ggtree",
      "role": "Imports"
    },
    {
      "package": "msa",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "phangorn",
      "role": "Imports"
    },
    {
      "package": "stringdist",
      "role": "Imports"
    },
    {
      "package": "UpSetR",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "pheatmap",
      "role": "Suggests"
    },
    {
      "package": "wordcloud",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "technology",
    "sequencing",
    "targetedresequencing",
    "alignment",
    "multiplesequencealignment"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 484,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 582,
    "source": "https://www.bioconductor.org/packages/stats/bioc/LymphoSeq"
  },
  "_mentions": 1,
  "_searchresults": 6,
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/LymphoSeq.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_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"
  ],
  "_help": [
    {
      "page": "alignSeq",
      "title": "Align mutliple sequences",
      "topics": [
        "alignSeq"
      ]
    },
    {
      "page": "bhattacharyyaCoefficient",
      "title": "Bhattacharyya coefficient",
      "topics": [
        "bhattacharyyaCoefficient"
      ]
    },
    {
      "page": "bhattacharyyaMatrix",
      "title": "Bhattacharyya matrix",
      "topics": [
        "bhattacharyyaMatrix"
      ]
    },
    {
      "page": "chordDiagramVDJ",
      "title": "Chord diagram of VJ or DJ gene associations",
      "topics": [
        "chordDiagramVDJ"
      ]
    },
    {
      "page": "clonality",
      "title": "Clonality",
      "topics": [
        "clonality"
      ]
    },
    {
      "page": "clonalRelatedness",
      "title": "Clonal relatedness",
      "topics": [
        "clonalRelatedness"
      ]
    },
    {
      "page": "cloneTrack",
      "title": "Clone tracking plot",
      "topics": [
        "cloneTrack"
      ]
    },
    {
      "page": "commonSeqs",
      "title": "Common sequences in two or more samples",
      "topics": [
        "commonSeqs"
      ]
    },
    {
      "page": "commonSeqsBar",
      "title": "Common sequences bar plot",
      "topics": [
        "commonSeqsBar"
      ]
    },
    {
      "page": "commonSeqsPlot",
      "title": "Common sequences plot",
      "topics": [
        "commonSeqsPlot"
      ]
    },
    {
      "page": "commonSeqsVenn",
      "title": "Common sequences Venn diagram",
      "topics": [
        "commonSeqsVenn"
      ]
    },
    {
      "page": "differentialAbundance",
      "title": "Differential abundance analysis",
      "topics": [
        "differentialAbundance"
      ]
    },
    {
      "page": "exportFasta",
      "title": "Export sequences in fasta format",
      "topics": [
        "exportFasta"
      ]
    },
    {
      "page": "geneFreq",
      "title": "Gene frequencies",
      "topics": [
        "geneFreq"
      ]
    },
    {
      "page": "lorenzCurve",
      "title": "Lorenz curve",
      "topics": [
        "lorenzCurve"
      ]
    },
    {
      "page": "mergeFiles",
      "title": "Merge files",
      "topics": [
        "mergeFiles"
      ]
    },
    {
      "page": "pairwisePlot",
      "title": "Pairwise comparison plot",
      "topics": [
        "pairwisePlot"
      ]
    },
    {
      "page": "phyloTree",
      "title": "Create phylogenetic tree",
      "topics": [
        "phyloTree"
      ]
    },
    {
      "page": "productive",
      "title": "Productive sequences",
      "topics": [
        "productive"
      ]
    },
    {
      "page": "productiveSeq",
      "title": "Productive sequences",
      "topics": [
        "productiveSeq"
      ]
    },
    {
      "page": "readImmunoSeq",
      "title": "Read ImmunoSeq files",
      "topics": [
        "readImmunoSeq"
      ]
    },
    {
      "page": "removeSeq",
      "title": "Remove sequence",
      "topics": [
        "removeSeq"
      ]
    },
    {
      "page": "searchPublished",
      "title": "Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity",
      "topics": [
        "searchPublished"
      ]
    },
    {
      "page": "searchSeq",
      "title": "Search for a sequence",
      "topics": [
        "searchSeq"
      ]
    },
    {
      "page": "seqMatrix",
      "title": "Sequence matrix",
      "topics": [
        "seqMatrix"
      ]
    },
    {
      "page": "similarityMatrix",
      "title": "Similarity score matrix",
      "topics": [
        "similarityMatrix"
      ]
    },
    {
      "page": "similarityScore",
      "title": "Similarity score",
      "topics": [
        "similarityScore"
      ]
    },
    {
      "page": "topFreq",
      "title": "Top frequencies",
      "topics": [
        "topFreq"
      ]
    },
    {
      "page": "topSeqs",
      "title": "Top sequences",
      "topics": [
        "topSeqs"
      ]
    },
    {
      "page": "topSeqsPlot",
      "title": "Cumulative frequency bar plot of top sequences",
      "topics": [
        "topSeqsPlot"
      ]
    },
    {
      "page": "uniqueSeqs",
      "title": "Unique sequences",
      "topics": [
        "uniqueSeqs"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/LymphoSeq/raw/HEAD/README.md",
  "_rundeps": [
    "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",
    "MultipleAlignment",
    "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"
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "lymphoseq",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-11-04T09:10:23.000Z",
      "distro": "resolute",
      "commit": "c95de6d86903ff4c15fe7900606d6f59ab394102",
      "fileid": "https://r2.ropensci.org/a0dba24c356ab117ce524d184c7b6d620eec40ed07d4c86f211b76be4b55c4a6",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-11-04T09:09:52.000Z",
      "distro": "resolute",
      "commit": "c95de6d86903ff4c15fe7900606d6f59ab394102",
      "fileid": "https://r2.ropensci.org/8bc9f9c303fbc3fd950745efd6ad239154bc5f148f499a8205405aaabf602052",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-11-04T09:09:00.000Z",
      "commit": "c95de6d86903ff4c15fe7900606d6f59ab394102",
      "fileid": "https://r2.ropensci.org/ca786bd4e22cb2a78db7954f27eb40f21c706dfffac74f594868d27d4c001447",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-11-04T09:09:21.000Z",
      "commit": "c95de6d86903ff4c15fe7900606d6f59ab394102",
      "fileid": "https://r2.ropensci.org/09629663d88f4010f35d4c6a5973830f6b6ac397236d0f852e21bf88b4f06117",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-11-04T09:08:28.000Z",
      "commit": "c95de6d86903ff4c15fe7900606d6f59ab394102",
      "fileid": "https://r2.ropensci.org/8a722401d184b5a5f3cb6b834adfbe2f685fd8bbbe07554112ca84cf1f502f16",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-11-04T09:07:36.000Z",
      "commit": "c95de6d86903ff4c15fe7900606d6f59ab394102",
      "fileid": "https://r2.ropensci.org/74a32b01b6c6523a4fcc51e27946f57602bf08bf55dbe8aa82f0b02924893ce8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-11-04T09:07:44.000Z",
      "commit": "c95de6d86903ff4c15fe7900606d6f59ab394102",
      "fileid": "https://r2.ropensci.org/f6631b48864ee3140fd6b3fa46b4626ba89bb4a3e2a026bf0ac3b1a812b67455",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-11-04T09:07:30.000Z",
      "commit": "c95de6d86903ff4c15fe7900606d6f59ab394102",
      "fileid": "https://r2.ropensci.org/29d37a95519501bdd2c4f455210d1e3f662495887809d466015b85125fb1b4f1",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41803876714"
    }
  ]
}