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 preinstalled IgBLAST-compatible
        germline databases from OGRDB, the AIRR Community’s Open
        Germline Receptor Database, for various organisms. It provides
        functions to install additional IgBLAST-compatible germline
        databases using reference sequences retrieved from IMGT/V-QUEST
        or OGRDB, or from 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: 1.2.19
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: Peptides, 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
        load_intdata.R load_auxdata.R intdata-misc.R auxdata-misc.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
        extract_sequence_region.R percent_mutation.R
        summarizeMismatches.R net_charge.R OAS-utils.R zzz.R
Config/pak/sysreqs: libxml2-dev libssl-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-08-09 22:13:49 UTC
RemoteUrl: https://github.com/bioc/igblastr
RemoteRef: RELEASE_3_23
RemoteSha: 77f1097300312ef40db070fbe40af005df082534
NeedsCompilation: no
Packaged: 2026-08-10 05:22:05 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 4.6.1; ; 2026-08-10 05:28:10 UTC; unix
