Package: igblastr
Title: User-friendly R Wrapper to IgBLAST
Description: The igblastr package provides functions to conveniently
        install and use a local IgBLAST installation from within R. The
        package also includes a set of built-in IgBLAST-compatible
        germline databases from OGRDB, the AIRR Community’s Open
        Germline Receptor Database, for various organisms. It provides
        functions to create additional IgBLAST-compatible germline
        databases using reference sequences retrieved from IMGT/V-QUEST
        or local FASTA files supplied by the user. When possible,
        annotations for the V and J alleles in a new germline database
        are automatically generated and added to the database, so they
        can be used as replacements for the internal and auxiliary data
        provided by IgBLAST. IgBLAST is described at
        <https://pubmed.ncbi.nlm.nih.gov/23671333/>. IgBLAST web
        interface: <https://www.ncbi.nlm.nih.gov/igblast/>. OGRDB:
        <https://ogrdb.airr-community.org/>. IMGT/V-QUEST download
        site: <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: 1.3.11
License: Artistic-2.0
Encoding: UTF-8
Authors@R: c(
	person("Hervé", "Pagès", role=c("aut", "cre"),
	       email="hpages.on.github@gmail.com",
	       comment=c(ORCID="0009-0002-8272-4522")),
	person("Ollivier", "Hyrien", role=c("aut", "fnd"),
	       comment=c(ORCID="0000-0003-1909-2542")),
	person("Kellie", "MacPhee", role="ctb",
	       comment=c(ORCID="0009-0008-0993-4009")),
	person("Michael", "Duff", role="ctb",
	       comment=c(ORCID="0009-0008-4279-0756")),
	person("Jason", "Taylor", role="ctb"))
Depends: R (>= 4.2.0), tibble, Biostrings
Imports: methods, utils, stats, tools, R.utils, curl, httr, xml2,
        rvest, xtable, jsonlite, BiocGenerics, S4Vectors, IRanges,
        GenomeInfoDb
Suggests: GenomicAlignments, parallel, testthat, knitr, rmarkdown,
        BiocStyle, ggplot2, dplyr, scales, ggseqlogo, airr
VignetteBuilder: knitr
Collate: utils.R internet-utils.R long_to_wide_airr.R igdata-IO.R
        translate_codons.R allele2gene.R parse_imgt_fasta_headers.R
        file-utils.R loci-utils.R db-utils.R ndm_data-IO.R
        compute_V_gene_delineations.R auxdata-IO.R compute_auxdata.R
        clean_allele_set.R V_alleles-inspect.R J_alleles-inspect.R
        LATIN_NAMES.R IMGT-utils.R IMGT-c_region-utils.R
        precompiled-igblast-utils.R cache-utils.R get_igblast_root.R
        edit_imgt_file.R igblast_info.R update_live_igdata.R
        intdata-utils.R auxdata-utils.R install_igblast.R
        make_blastdbs.R create_region_db.R create_germline_db.R
        create_c_region_db.R reset_germline_dbs.R list_germline_dbs.R
        use_germline_db.R reset_c_region_dbs.R list_c_region_dbs.R
        use_c_region_db.R install_custom_germline_db.R OGRDB-utils.R
        OGRDB-API.R download_OGRDB_germline_sequences.R
        download_OGRDB_germline_json.R install_OGRDB_germline_db.R
        download_IMGT_germline_sequences.R install_IMGT_germline_db.R
        combine_germline_dbs.R augment_germline_db.R
        prepare_igblastn_cmdline_args.R read_igblastn_fmt7_output.R
        read_igblastn_AIRR_output.R igblastn.R igbrowser.R
        percent_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: 2026-06-17 01:43:39 UTC
RemoteUrl: https://github.com/bioc/igblastr
RemoteRef: HEAD
RemoteSha: 4f148d0aebf0ba041fe35c588785d9f5b1919038
NeedsCompilation: no
Packaged: 2026-06-17 06:16:25 UTC; root
Author: Hervé Pagès [aut, cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>),
  Ollivier Hyrien [aut, fnd] (ORCID:
    <https://orcid.org/0000-0003-1909-2542>),
  Kellie MacPhee [ctb] (ORCID: <https://orcid.org/0009-0008-0993-4009>),
  Michael Duff [ctb] (ORCID: <https://orcid.org/0009-0008-4279-0756>),
  Jason Taylor [ctb]
Maintainer: Hervé Pagès <hpages.on.github@gmail.com>
Built: R 4.6.0; ; 2026-06-17 06:19:52 UTC; windows
