{
  "_id": "6a2161d6cd65a98ecbd32087",
  "Package": "igblastr",
  "Title": "User-friendly R Wrapper to IgBLAST",
  "Description": "The igblastr package provides functions to conveniently\ninstall and use a local IgBLAST installation from within R. The\npackage also includes a set of built-in IgBLAST-compatible\ngermline databases from OGRDB, the AIRR Community’s Open\nGermline Receptor Database, for various organisms. It provides\nfunctions to create additional IgBLAST-compatible germline\ndatabases using reference sequences retrieved from IMGT/V-QUEST\nor local FASTA files supplied by the user. When possible,\nannotations for the V and J alleles in a new germline database\nare automatically computed and added to the database, so they\ncan be used as replacements for the internal and auxiliary data\nshipped with IgBLAST. IgBLAST is described at\n<https://pubmed.ncbi.nlm.nih.gov/23671333/>. IgBLAST web\ninterface: <https://www.ncbi.nlm.nih.gov/igblast/>. OGRDB:\n<https://ogrdb.airr-community.org/>. IMGT/V-QUEST download\nsite: <https://www.imgt.org/download/V-QUEST/>.",
  "biocViews": "Immunology, Immunogenetics, ImmunoOncology, CellBiology",
  "URL": "https://bioconductor.org/packages/igblastr",
  "BugReports": "https://github.com/HyrienLab/igblastr/issues",
  "Version": "1.3.7",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\",\ncomment=c(ORCID=\"0009-0002-8272-4522\")),\nperson(\"Ollivier\", \"Hyrien\", role=c(\"aut\", \"fnd\"),\ncomment=c(ORCID=\"0000-0003-1909-2542\")),\nperson(\"Kellie\", \"MacPhee\", role=\"ctb\",\ncomment=c(ORCID=\"0009-0008-0993-4009\")),\nperson(\"Michael\", \"Duff\", role=\"ctb\",\ncomment=c(ORCID=\"0009-0008-4279-0756\")),\nperson(\"Jason\", \"Taylor\", role=\"ctb\"))",
  "VignetteBuilder": "knitr",
  "Collate": "utils.R internet-utils.R long_to_wide_airr.R igdata-IO.R\ntranslate_codons.R allele2gene.R parse_imgt_fasta_headers.R\nfile-utils.R loci-utils.R db-utils.R ndm_data-IO.R\ncompute_V_gene_delineations.R auxdata-IO.R compute_auxdata.R\nclean_allele_set.R V_alleles-inspect.R J_alleles-inspect.R\nLATIN_NAMES.R IMGT-utils.R IMGT-c_region-utils.R\nprecompiled-igblast-utils.R cache-utils.R get_igblast_root.R\nedit_imgt_file.R igblast_info.R update_live_igdata.R\nintdata-utils.R auxdata-utils.R install_igblast.R\nmake_blastdbs.R create_region_db.R create_germline_db.R\ncreate_c_region_db.R reset_germline_dbs.R list_germline_dbs.R\nuse_germline_db.R reset_c_region_dbs.R list_c_region_dbs.R\nuse_c_region_db.R install_custom_germline_db.R OGRDB-utils.R\nOGRDB-API.R download_OGRDB_germline_sequences.R\ndownload_OGRDB_germline_json.R install_OGRDB_germline_db.R\ndownload_IMGT_germline_sequences.R install_IMGT_germline_db.R\ncombine_germline_dbs.R augment_germline_db.R\nprepare_igblastn_cmdline_args.R read_igblastn_fmt7_output.R\nread_igblastn_AIRR_output.R igblastn.R igbrowser.R\npercent_mutation.R summarizeMismatches.R OAS-utils.R zzz.R",
  "Config/Bioconductor/UnsupportedPlatforms": "aarch64-linux-gnu",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-04 02:55:08 UTC",
  "RemoteUrl": "https://github.com/bioc/igblastr",
  "RemoteRef": "HEAD",
  "RemoteSha": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 11:10:12 UTC",
    "User": "root"
  },
  "Author": "Hervé Pagès [aut, cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>),\nOllivier Hyrien [aut, fnd] (ORCID:\n<https://orcid.org/0000-0003-1909-2542>),\nKellie MacPhee [ctb] (ORCID: <https://orcid.org/0009-0008-0993-4009>),\nMichael Duff [ctb] (ORCID: <https://orcid.org/0009-0008-4279-0756>),\nJason Taylor [ctb]",
  "Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>",
  "MD5sum": "91e011fe0b56023c527805be7cf10906",
  "_user": "bioc",
  "_type": "src",
  "_file": "igblastr_1.3.7.tar.gz",
  "_fileid": "ebb7411d26f08023e1b167f457077e154aab049e5186a20963aaeb2253b010e3",
  "_filesize": 4941370,
  "_sha256": "ebb7411d26f08023e1b167f457077e154aab049e5186a20963aaeb2253b010e3",
  "_created": "2026-06-04T11:10:12.000Z",
  "_published": "2026-06-04T11:30:30.821Z",
  "_jobs": [
    {
      "job": 79506101832,
      "time": 186,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7409962501"
    },
    {
      "job": 79506101813,
      "time": 543,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7410076729"
    },
    {
      "job": 79506101753,
      "time": 637,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7410107104"
    },
    {
      "job": 79506101778,
      "time": 235,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7410168941"
    },
    {
      "job": 79506101737,
      "time": 488,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7410270748"
    },
    {
      "job": 79504911222,
      "time": 451,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7409901774"
    },
    {
      "job": 79506101732,
      "time": 144,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7409949023"
    },
    {
      "job": 79506101767,
      "time": 617,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7410100754"
    },
    {
      "job": 79506101756,
      "time": 343,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7410013701"
    },
    {
      "job": 79506101746,
      "time": 692,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7410125327"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 4,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/igblastr",
  "_commit": {
    "id": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
    "author": "Hervé Pagès <hpages.on.github@gmail.com>",
    "committer": "Hervé Pagès <hpages.on.github@gmail.com>",
    "message": "document how percent_mutation() computes the percent mutation\n",
    "time": 1780541708
  },
  "_maintainer": {
    "name": "Hervé Pagès",
    "email": "hpages.on.github@gmail.com",
    "login": "hpages",
    "linkedin": "in/hervé-pagès-5038527",
    "description": "",
    "uuid": 8810451
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "tibble",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "curl",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "rvest",
      "role": "Imports"
    },
    {
      "package": "xtable",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    },
    {
      "package": "ggseqlogo",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-23",
      "n": 1
    },
    {
      "week": "2025-24",
      "n": 4
    },
    {
      "week": "2025-25",
      "n": 6
    },
    {
      "week": "2025-32",
      "n": 2
    },
    {
      "week": "2025-33",
      "n": 1
    },
    {
      "week": "2025-34",
      "n": 2
    },
    {
      "week": "2025-35",
      "n": 2
    },
    {
      "week": "2025-36",
      "n": 4
    },
    {
      "week": "2025-37",
      "n": 4
    },
    {
      "week": "2025-41",
      "n": 4
    },
    {
      "week": "2025-43",
      "n": 4
    },
    {
      "week": "2025-44",
      "n": 3
    },
    {
      "week": "2025-46",
      "n": 4
    },
    {
      "week": "2025-47",
      "n": 3
    },
    {
      "week": "2025-48",
      "n": 1
    },
    {
      "week": "2025-49",
      "n": 2
    },
    {
      "week": "2025-50",
      "n": 5
    },
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2026-01",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 5
    },
    {
      "week": "2026-03",
      "n": 2
    },
    {
      "week": "2026-04",
      "n": 7
    },
    {
      "week": "2026-07",
      "n": 5
    },
    {
      "week": "2026-08",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 10
    },
    {
      "week": "2026-10",
      "n": 4
    },
    {
      "week": "2026-11",
      "n": 5
    },
    {
      "week": "2026-12",
      "n": 3
    },
    {
      "week": "2026-15",
      "n": 6
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-17",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 7
    },
    {
      "week": "2026-20",
      "n": 2
    },
    {
      "week": "2026-21",
      "n": 4
    },
    {
      "week": "2026-22",
      "n": 5
    },
    {
      "week": "2026-23",
      "n": 4
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.3.5",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.2.5",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunology",
    "immunogenetics",
    "immunooncology",
    "cellbiology",
    "bioconductor-package"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "hpages",
      "count": 251,
      "uuid": 8810451
    },
    {
      "user": "ohyrien",
      "count": 9,
      "uuid": 28492020
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "kelliemac",
      "count": 1,
      "uuid": 25042566
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 214,
    "source": "https://www.bioconductor.org/packages/stats/bioc/igblastr"
  },
  "_devurl": "https://github.com/hyrienlab/igblastr",
  "_searchresults": 20,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/igblastr.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/hyrienlab/igblastr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "allele2gene",
    "augment_germline_db_D",
    "augment_germline_db_J",
    "augment_germline_db_V",
    "bcr_browser",
    "combine_c_region_dbs",
    "combine_germline_dbs",
    "compute_auxdata",
    "compute_germline_db_auxdata",
    "compute_imgt_intdata",
    "compute_V_gene_delineations",
    "download_IMGT_germline_sequences",
    "download_OGRDB_germline_json",
    "download_OGRDB_germline_sequences",
    "download_paired_OAS_units",
    "extract_auxdata_from_ogrdb_json",
    "extract_codons",
    "extract_intdata_from_ogrdb_json",
    "extract_metadata_from_OAS_units",
    "extract_sequences_from_paired_OAS_df",
    "extract_sequences_from_paired_OAS_units",
    "get_auxdata_path",
    "get_igblast_auxiliary_data",
    "get_igblast_root",
    "get_intdata_path",
    "has_igblast",
    "igblast_build",
    "igblast_info",
    "igblastn",
    "igblastn_help",
    "igblastn_version",
    "igbrowser",
    "igdata_info",
    "IMGT_is_up",
    "infer_cdr3_ends_via_fwr4_comparisons",
    "install_custom_germline_db",
    "install_igblast",
    "install_IMGT_c_region_db",
    "install_IMGT_germline_db",
    "J_allele_has_stop_codon",
    "list_c_region_dbs",
    "list_germline_dbs",
    "list_igblast_organisms",
    "list_IMGT_organisms",
    "list_IMGT_releases",
    "list_outfmt7_specifiers",
    "list_paired_OAS_studies",
    "list_paired_OAS_units",
    "load_auxdata",
    "load_c_region_db",
    "load_c_region_sequences",
    "load_germline_db",
    "load_germline_sequences",
    "load_igblast_auxiliary_data",
    "load_intdata",
    "makeblastdb_version",
    "OAS_is_up",
    "parse_imgt_fasta_headers",
    "parse_outfmt7",
    "percent_mutation",
    "print_J_alleles",
    "print.alignment_summary",
    "print.auxdata_md5sum_df",
    "print.c_region_dbs_df",
    "print.fmt7footer",
    "print.fmt7record",
    "print.germline_dbs_df",
    "print.hit_table",
    "print.igblast_info",
    "print.igblastn_raw_output",
    "print.igdata_info",
    "print.outfmt7_specifiers",
    "print.query_details",
    "print.subregion_sequence_details",
    "print.VDJ_junction_details",
    "print.VDJ_rearrangement_summary",
    "qseqid",
    "qseqid.fmt7record",
    "qseqid.query_details",
    "read_auxdata",
    "read_igblastn_AIRR_output",
    "read_igblastn_fmt7_output",
    "read_ndm_data",
    "read_OAS_csv",
    "read_OAS_csv_metadata",
    "remove_gaps",
    "reset_c_region_dbs",
    "reset_germline_dbs",
    "reset_live_igdata",
    "rm_c_region_db",
    "rm_germline_db",
    "same_alleles_annot",
    "set_igblast_root",
    "show_intdata_disagreements",
    "summary.query_details",
    "tabulate_deletions",
    "tabulate_insertions",
    "tabulate_mismatches",
    "time_since_live_igdata_last_checked",
    "translate_codons",
    "translate_fwr4",
    "translate_J_alleles",
    "translate_V_alleles",
    "update_live_igdata",
    "use_c_region_db",
    "use_germline_db",
    "V_allele_has_stop_codon",
    "V_genes_with_varying_fwrcdr_boundaries",
    "validate_ndm_rows",
    "write_auxdata",
    "write_ndm_data"
  ],
  "_help": [
    {
      "page": "allele2gene",
      "title": "Go from germline gene allele names to germline gene names",
      "topics": [
        "allele2gene"
      ]
    },
    {
      "page": "augment_germline_db",
      "title": "Add novel gene alleles to a germline db",
      "topics": [
        "augment_germline_db",
        "augment_germline_db_D",
        "augment_germline_db_J",
        "augment_germline_db_V"
      ]
    },
    {
      "page": "auxdata-IO",
      "title": "Read/write IgBLAST auxiliary data files",
      "topics": [
        "auxdata-IO",
        "auxdata_IO",
        "read_auxdata",
        "write_auxdata"
      ]
    },
    {
      "page": "auxdata-utils",
      "title": "Access IgBLAST auxiliary data",
      "topics": [
        "auxdata",
        "auxdata-utils",
        "auxdata_utils",
        "compute_germline_db_auxdata",
        "get_auxdata_path",
        "get_igblast_auxiliary_data",
        "load_auxdata",
        "load_igblast_auxiliary_data"
      ]
    },
    {
      "page": "combine_germline_dbs",
      "title": "Combine two existing germline dbs",
      "topics": [
        "combine_c_region_dbs",
        "combine_germline_dbs"
      ]
    },
    {
      "page": "compute_auxdata",
      "title": "Compute IgBLAST auxiliary data",
      "topics": [
        "compute_auxdata",
        "infer_cdr3_ends_via_fwr4_comparisons"
      ]
    },
    {
      "page": "compute_V_gene_delineations",
      "title": "Compute V gene delineations",
      "topics": [
        "compute_imgt_intdata",
        "compute_V_gene_delineations"
      ]
    },
    {
      "page": "download_IMGT_germline_sequences",
      "title": "Download germline sequences from IMGT",
      "topics": [
        "download_IMGT_germline_sequences",
        "IMGT_is_up",
        "list_IMGT_organisms",
        "list_IMGT_releases"
      ]
    },
    {
      "page": "download_OGRDB_germline_json",
      "title": "Download AIRR-C JSON files from OGRDB",
      "topics": [
        "download_OGRDB_germline_json",
        "extract_auxdata_from_ogrdb_json",
        "extract_intdata_from_ogrdb_json"
      ]
    },
    {
      "page": "download_OGRDB_germline_sequences",
      "title": "Download germline sequences from OGRDB",
      "topics": [
        "download_OGRDB_germline_sequences"
      ]
    },
    {
      "page": "get_igblast_root",
      "title": "Control IgBLAST installation to use",
      "topics": [
        "get_igblast_root",
        "set_igblast_root"
      ]
    },
    {
      "page": "igblast_info",
      "title": "Check IgBLAST used by igblastr",
      "topics": [
        "has_igblast",
        "igblastn_version",
        "igblast_build",
        "igblast_info",
        "list_igblast_organisms",
        "makeblastdb_version",
        "print.igblast_info"
      ]
    },
    {
      "page": "IGBLAST_ROOT",
      "title": "Use an external IgBLAST installation",
      "topics": [
        "IGBLAST_ROOT"
      ]
    },
    {
      "page": "igblastn",
      "title": "BLAST for BCR/Ig and TCR sequences",
      "topics": [
        "igblastn",
        "igblastn_help",
        "print.igblastn_raw_output"
      ]
    },
    {
      "page": "igblastr_usage_report",
      "title": "Turn \"Usage Reporting\" on or off",
      "topics": [
        "BLAST_USAGE_REPORT",
        "igblastr_usage_report",
        "Usage_report",
        "usage_report",
        "Usage_reporting",
        "usage_reporting"
      ]
    },
    {
      "page": "igbrowser",
      "title": "Display annotated BCR sequences in a browser",
      "topics": [
        "bcr_browser",
        "igbrowser"
      ]
    },
    {
      "page": "install_custom_germline_db",
      "title": "Install a germline db from user-supplied gene allele sequences",
      "topics": [
        "install_custom_germline_db"
      ]
    },
    {
      "page": "install_igblast",
      "title": "Install IgBLAST",
      "topics": [
        "install_igblast"
      ]
    },
    {
      "page": "install_IMGT_germline_db",
      "title": "Install a germline db from IMGT",
      "topics": [
        "install_IMGT_c_region_db",
        "install_IMGT_germline_db"
      ]
    },
    {
      "page": "intdata-utils",
      "title": "Access IgBLAST internal data",
      "topics": [
        "get_intdata_path",
        "intdata",
        "intdata-utils",
        "intdata_utils",
        "load_intdata",
        "show_intdata_disagreements",
        "V_genes_with_varying_fwrcdr_boundaries"
      ]
    },
    {
      "page": "J_alleles-inspect",
      "title": "Basic inspection of J allele sequences",
      "topics": [
        "J_alleles-inspect",
        "J_alleles_inspect",
        "J_allele_has_stop_codon",
        "print_J_alleles",
        "translate_fwr4",
        "translate_J_alleles"
      ]
    },
    {
      "page": "list_c_region_dbs",
      "title": "List cached C-region dbs",
      "topics": [
        "list_c_region_dbs",
        "print.c_region_dbs_df",
        "rm_c_region_db"
      ]
    },
    {
      "page": "list_germline_dbs",
      "title": "List cached germline dbs",
      "topics": [
        "list_germline_dbs",
        "print.germline_dbs_df",
        "rm_germline_db"
      ]
    },
    {
      "page": "ndm_data-IO",
      "title": "Read/write \"ndm\" files",
      "topics": [
        "ndm_data-IO",
        "ndm_data_IO",
        "read_ndm_data",
        "same_alleles_annot",
        "validate_ndm_rows",
        "write_ndm_data"
      ]
    },
    {
      "page": "OAS-utils",
      "title": "Download and manipulate OAS data",
      "topics": [
        "download_paired_OAS_units",
        "extract_metadata_from_OAS_units",
        "extract_sequences_from_paired_OAS_df",
        "extract_sequences_from_paired_OAS_units",
        "list_paired_OAS_studies",
        "list_paired_OAS_units",
        "OAS-utils",
        "OAS_is_up",
        "OAS_utils",
        "read_OAS_csv",
        "read_OAS_csv_metadata"
      ]
    },
    {
      "page": "parse_imgt_fasta_headers",
      "title": "Parse IMGT FASTA headers",
      "topics": [
        "parse_imgt_fasta_headers"
      ]
    },
    {
      "page": "percent_mutation",
      "title": "Computes percent mutation in V, D, J segments",
      "topics": [
        "percent_mutation"
      ]
    },
    {
      "page": "read_igblastn_AIRR_output",
      "title": "igblastn output format 19 (AIRR format)",
      "topics": [
        "read_igblastn_AIRR_output"
      ]
    },
    {
      "page": "read_igblastn_fmt7_output",
      "title": "igblastn output format 7",
      "topics": [
        "fmt7-utils",
        "fmt7_utils",
        "list_outfmt7_specifiers",
        "outfmt7-utils",
        "outfmt7_utils",
        "parse_outfmt7",
        "print.alignment_summary",
        "print.fmt7footer",
        "print.fmt7record",
        "print.hit_table",
        "print.outfmt7_specifiers",
        "print.query_details",
        "print.subregion_sequence_details",
        "print.VDJ_junction_details",
        "print.VDJ_rearrangement_summary",
        "qseqid",
        "qseqid.fmt7record",
        "qseqid.query_details",
        "read_igblastn_fmt7_output",
        "summary.query_details"
      ]
    },
    {
      "page": "reset_c_region_dbs",
      "title": "Reset the cached C-region dbs",
      "topics": [
        "reset_c_region_dbs"
      ]
    },
    {
      "page": "reset_germline_dbs",
      "title": "Reset the cached germline dbs",
      "topics": [
        "reset_germline_dbs"
      ]
    },
    {
      "page": "summarizeMismatches",
      "title": "Summarize mismatches and indels between query and germline sequences",
      "topics": [
        "summarizeMismatches",
        "tabulate_deletions",
        "tabulate_insertions",
        "tabulate_mismatches"
      ]
    },
    {
      "page": "translate_codons",
      "title": "Extract and translate codons from a set of DNA sequences",
      "topics": [
        "extract_codons",
        "remove_gaps",
        "translate_codons"
      ]
    },
    {
      "page": "update_live_igdata",
      "title": "Update and manage IgBLAST auxiliary and internal data",
      "topics": [
        "igdata_info",
        "live_igdata",
        "print.auxdata_md5sum_df",
        "print.igdata_info",
        "reset_live_igdata",
        "time_since_live_igdata_last_checked",
        "update_live_igdata"
      ]
    },
    {
      "page": "use_c_region_db",
      "title": "Select cached C-region db to use with igblastn()",
      "topics": [
        "load_c_region_db",
        "load_c_region_sequences",
        "use_c_region_db"
      ]
    },
    {
      "page": "use_germline_db",
      "title": "Select cached germline db to use with igblastn()",
      "topics": [
        "load_germline_db",
        "load_germline_sequences",
        "use_germline_db"
      ]
    },
    {
      "page": "V_alleles-inspect",
      "title": "Basic inspection of V allele sequences",
      "topics": [
        "translate_V_alleles",
        "V_alleles-inspect",
        "V_alleles_inspect",
        "V_allele_has_stop_codon"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/igblastr/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "BiocGenerics",
    "Biostrings",
    "cli",
    "crayon",
    "curl",
    "generics",
    "GenomeInfoDb",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rlang",
    "rvest",
    "S4Vectors",
    "selectr",
    "Seqinfo",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "xml2",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "igblastr_overview.Rmd",
      "filename": "igblastr_overview.html",
      "title": "igblastr overview",
      "author": "Hervé Pagès, Kellie MacPhee, Ollivier Hyrien",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Install and load the package",
        "Install IgBLAST",
        "Install and select a germline database",
        "Built-in germline databases",
        "Install additional germline databases",
        "Install germline database from IMGT/V-QUEST",
        "Internal data and auxiliary data",
        "Install germline database from user-supplied gene allele sequences",
        "Selecting a germline database to use with igblastn()",
        "Selecting a constant region database (optional)",
        "Use igblastn()",
        "Downstream analysis examples",
        "Advanced usage",
        "Passing additional arguments to igblastn()",
        "Restrict the search to a subset of user-supplied gene alleles",
        "A TCR analysis example",
        "Future developments",
        "Session information"
      ],
      "created": "2025-03-26 19:33:24",
      "modified": "2026-06-03 07:24:06",
      "commits": 42
    }
  ],
  "_score": 6.635483746814913,
  "_indexed": true,
  "_nocasepkg": "igblastr",
  "_universes": [
    "bioc",
    "hpages",
    "hyrienlab"
  ],
  "_previous": "1.3.6",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.7",
      "date": "2026-06-04T11:13:29.000Z",
      "distro": "noble",
      "commit": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
      "fileid": "a016a37564c59a5554acca55633cad63e4505ef434a5b2fdfc8680ec2866f1e2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.7",
      "date": "2026-06-04T11:15:08.000Z",
      "distro": "noble",
      "commit": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
      "fileid": "b3bcfbfc309f8abb6a87a68e317a144643b147494dad96998c463f3c6a4ffb30",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.7",
      "date": "2026-06-04T11:22:30.000Z",
      "commit": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
      "fileid": "c325fcce2dfda1933f85a661423427545b2cd2439fee8724813ffbe71e4a5d36",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.7",
      "date": "2026-06-04T11:23:45.000Z",
      "commit": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
      "fileid": "628de4a5bc83283ce1f24ea1f55248bf472425d521af93375d020a7d3c71fce3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.7",
      "date": "2026-06-04T11:13:07.000Z",
      "commit": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
      "fileid": "aa4e3efdcfdb3b64b1d2e106969fbb3353a6f505ec79ba3dff4d6fd3cfd1843a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.7",
      "date": "2026-06-04T11:12:23.000Z",
      "commit": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
      "fileid": "6082d52a55746e9f6af459acab7099f49608618135dd72c810213597e815768a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.7",
      "date": "2026-06-04T11:12:10.000Z",
      "commit": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
      "fileid": "851e8e3d9fce5dc08007e630fb7b0610aba101e9d71775494668c3403e3057ab",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.7",
      "date": "2026-06-04T11:12:24.000Z",
      "commit": "f7a36ebfa184eb0129edb35a14c76eb5f645a6a7",
      "fileid": "c23fffad6e071b8b809a0f2db6c03bb88d2c56e484a2c6e88a30fea4c446cbc3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26947750137"
    }
  ]
}