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, the
        FWR/CDR boundaries on the V alleles (a.k.a "internal data") are
        computed and stored in the germline database, so can be used as
        a replacement for the internal data shipped with 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: 1.2.0
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, S4Vectors, IRanges, GenomeInfoDb
Suggests: GenomicAlignments, parallel, testthat, knitr, rmarkdown,
        BiocStyle, ggplot2, dplyr, scales, ggseqlogo
VignetteBuilder: knitr
Collate: utils.R internet-utils.R long_to_wide_airr.R
        read_broken_table.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 clean_allele_set.R
        auxdata-IO.R compute_auxdata.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
        augment_germline_db.R prepare_igblastn_cmdline_args.R
        read_igblastn_fmt7_output.R read_igblastn_AIRR_output.R
        igblastn.R igbrowser.R summarizeMismatches.R OAS-utils.R zzz.R
Config/pak/sysreqs: libicu-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-29 05:25:16 UTC
RemoteUrl: https://github.com/bioc/igblastr
RemoteRef: RELEASE_3_23
RemoteSha: 761b35cd640db5a13d939f849c0bbbdfc980236c
NeedsCompilation: no
Packaged: 2026-04-29 22:25:31 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; ; 2026-04-29 22:27:53 UTC; windows
