{
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  "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 preinstalled IgBLAST-compatible\ngermline databases from OGRDB, the AIRR Community’s Open\nGermline Receptor Database, for various organisms. It provides\nfunctions to install additional IgBLAST-compatible germline\ndatabases using reference sequences retrieved from IMGT/V-QUEST\nor OGRDB, or from local FASTA files supplied by the user. When\npossible, annotations for the V and J alleles in a new germline\ndatabase are automatically generated and added to the database,\nso they can be used as replacements for the internal and\nauxiliary data provided by 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": "1.3.24",
  "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\"))",
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  "Collate": "utils.R ascii-viz-utils.R internet-utils.R long_to_wide_airr.R\ntranslate_codons.R allele2gene.R parse_imgt_fasta_headers.R\nigdata-utils.R file-utils.R loci-utils.R db-utils.R\nndm_data-IO.R compute_V_gene_delineations.R auxdata-IO.R\ncompute_auxdata.R clean_allele_set.R V_alleles-inspect.R\nJ_alleles-inspect.R LATIN_NAMES.R IMGT-utils.R\nIMGT-intdata-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\nload_intdata.R load_auxdata.R intdata-misc.R auxdata-misc.R\ninstall_igblast.R make_blastdbs.R create_region_db.R\ncreate_germline_db.R create_c_region_db.R reset_germline_dbs.R\nlist_germline_dbs.R use_germline_db.R reset_c_region_dbs.R\nlist_c_region_dbs.R use_c_region_db.R\ninstall_custom_germline_db.R OGRDB-utils.R OGRDB-API.R\ndownload_OGRDB_germline_json.R\ndownload_OGRDB_germline_sequences.R\ndownload_IMGT_germline_sequences.R print_gapped_V_alleles.R\nprint_J_alleles.R install_OGRDB_germline_db.R\ninstall_IMGT_germline_db.R combine_germline_dbs.R\naugment_germline_db.R prepare_igblastn_cmdline_args.R\nread_igblastn_fmt7_output.R read_igblastn_AIRR_output.R\nigblastn.R igbrowser.R extract_sequence_region.R\npercent_mutation.R summarizeMismatches.R net_charge.R\nOAS-utils.R zzz.R",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-21 05:56:12 UTC",
  "RemoteUrl": "https://github.com/bioc/igblastr",
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  "NeedsCompilation": "no",
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    "Date": "2026-10-21 21:04:14 UTC",
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  "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>",
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  "_file": "igblastr_1.3.24.tar.gz",
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  "_created": "2026-10-21T21:04:14.000Z",
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    "augment_germline_db_J",
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    "download_OGRDB_germline_sequences",
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    "get_auxdata_path",
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    "list_c_region_dbs",
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      "title": "Go from germline gene allele names to germline gene names",
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      "title": "Add novel gene alleles to a germline db",
      "topics": [
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        "augment_germline_db_D",
        "augment_germline_db_J",
        "augment_germline_db_V"
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      "title": "Read/write IgBLAST auxiliary data files",
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        "auxdata_IO",
        "read_auxdata",
        "write_auxdata"
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    {
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      "title": "Miscellaneous auxiliary data utilities",
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        "auxdata_misc",
        "compute_germline_db_auxdata"
      ]
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      "title": "Combine two existing germline dbs",
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        "combine_germline_dbs"
      ]
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    {
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      "title": "Compute IgBLAST auxiliary data",
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        "solve_cdr3_ends_using_fwr4_aa_comparisons",
        "solve_cdr3_ends_using_fwr4_dna_comparisons",
        "solve_cdr3_ends_using_fwr4_dna_PWM",
        "validate_and_complete_auxdata_with_ref"
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        "compute_V_gene_delineations",
        "IMGT_DEFAULT_FWRCDR_WIDTHS"
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      "title": "Download germline sequences from IMGT",
      "topics": [
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        "IMGT_is_up",
        "list_IMGT_organisms",
        "list_IMGT_releases"
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      "topics": [
        "download_OGRDB_germline_json",
        "extract_alleles_from_ogrdb_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": "extract_sequence_region",
      "title": "Extract region of interest from a set of analyzed sequences",
      "topics": [
        "extract_region_length",
        "extract_sequence_region"
      ]
    },
    {
      "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": "IMGT-intdata-utils",
      "title": "Get the FWR/CDR widths for a given IMGT organism",
      "topics": [
        "get_fwrcdr_widths_for_imgt_organism",
        "IMGT-intdata-utils",
        "IMGT_intdata_utils"
      ]
    },
    {
      "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": "install_OGRDB_germline_db",
      "title": "Install a germline db from OGRDB germline sets",
      "topics": [
        "install_OGRDB_germline_db",
        "make_auxdata_files_from_ogrdb_jsons",
        "make_intdata_files_from_ogrdb_jsons"
      ]
    },
    {
      "page": "intdata-misc",
      "title": "Miscellaneous internal data utilities",
      "topics": [
        "intdata-misc",
        "intdata_misc",
        "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",
        "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": "load_auxdata",
      "title": "Access IgBLAST auxiliary data",
      "topics": [
        "auxdata",
        "get_auxdata_path",
        "get_igblast_auxiliary_data",
        "load_auxdata",
        "load_igblast_auxiliary_data"
      ]
    },
    {
      "page": "load_intdata",
      "title": "Access IgBLAST internal data",
      "topics": [
        "get_intdata_path",
        "intdata",
        "load_intdata"
      ]
    },
    {
      "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": "net_charge",
      "title": "Compute the net charges of amino acid sequences",
      "topics": [
        "extract_region_net_charge",
        "net_charge",
        "PKA_VALUES"
      ]
    },
    {
      "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": "print_gapped_V_alleles",
      "title": "Fancy display of V alleles sequences",
      "topics": [
        "print_gapped_V_alleles"
      ]
    },
    {
      "page": "print_J_alleles",
      "title": "Fancy display of J alleles sequences",
      "topics": [
        "print_J_alleles"
      ]
    },
    {
      "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": [
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    "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",
    "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 and check IgBLAST",
        "Install IgBLAST",
        "Check IgBLAST",
        "Install and select an IgBLAST-compatible germline database",
        "Preinstalled germline databases",
        "Install additional IgBLAST-compatible germline databases",
        "Install an IgBLAST-compatible germline database from IMGT/V-QUEST",
        "Install an IgBLAST-compatible germline database from user-supplied gene allele sequences",
        "Select the germline database to use with igblastn()",
        "Internal data and auxiliary data",
        "What are the internal data and auxiliary data?",
        "IgBLAST-provided internal/auxiliary data",
        "igblastr-generated internal/auxiliary data",
        "How is this data generated?",
        "How to use the igblastr-generated internal/auxiliary data with igblastr?",
        "Select a constant region database (optional)",
        "Use igblastn()",
        "Prepare the query sequences",
        "Call igblastn() on the query sequences",
        "Downstream analysis",
        "Distribution of percent mutation across BCR sequences",
        "Distribution of germline genes",
        "Lengths and motifs of CDR3 sequences",
        "Advanced usage",
        "Passing additional arguments to igblastn()",
        "Restrict the search to a subset of user-supplied gene alleles",
        "Combine germline databases from two different organisms",
        "Create the hybrid germline database",
        "A quick look at columns v_call, d_call, and j_call",
        "A TCR analysis example",
        "Prepare the TCR query sequences",
        "Install a TCR germline database",
        "Select a TCR constant region database (optional)",
        "Call igblastn() on the TCR query sequences",
        "Future developments and session information",
        "Future developments",
        "Session information"
      ],
      "created": "2025-03-26 19:33:24",
      "modified": "2026-09-18 00:38:55",
      "commits": 60
    }
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  "_indexed": true,
  "_nocasepkg": "igblastr",
  "_universes": [
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    "hyrienlab"
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