Package: immunotation
Type: Package
Title: Tools for working with diverse immune genes
Version: 1.18.0
Date: 2021-08-09
Authors@R: c(
    person("Katharina", "Imkeller", email = "ag.imkeller@gmail.com", role = c("cre", "aut")))
Description: MHC (major histocompatibility complex) molecules are cell
        surface complexes that present antigens to T cells.  The
        repertoire of antigens presented in a given genetic background
        largely depends on the sequence of the encoded MHC molecules,
        and thus, in humans, on the highly variable HLA (human
        leukocyte antigen) genes of the hyperpolymorphic HLA locus.
        More than 28,000 different HLA alleles have been reported, with
        significant differences in allele frequencies between human
        populations worldwide. Reproducible and consistent annotation
        of HLA alleles in large-scale bioinformatics workflows remains
        challenging, because the available reference databases and
        software tools often use different HLA naming schemes. The
        package immunotation provides tools for consistent annotation
        of HLA genes in typical immunoinformatics workflows such as for
        example the prediction of MHC-presented peptides in different
        human donors. Converter functions that provide mappings between
        different HLA naming schemes are based on the MHC restriction
        ontology (MRO). The package also provides automated access to
        HLA alleles frequencies in worldwide human reference
        populations stored in the Allele Frequency Net Database.
License: GPL-3
Encoding: UTF-8
Collate: 'external_resources_input.R' 'AFND_interface.R'
        'MRO_interface_helper.R' 'MRO_interface.R' 'MACUI_interface.R'
        'nomenclature_queries.R' 'AFND_queries.R' 'visualization.R'
Depends: R (>= 4.1)
Imports: stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr,
        xml2, maps, rlang
Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
VignetteBuilder: knitr
RoxygenNote: 7.1.1
biocViews: Software, ImmunoOncology, BiomedicalInformatics, Genetics,
        Annotation
BugReports: https://github.com/imkeller/immunotation/issues
Config/pak/sysreqs: libicu-dev libxml2-dev libssl-dev libx11-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:08:50 UTC
RemoteUrl: https://github.com/bioc/immunotation
RemoteRef: RELEASE_3_22
RemoteSha: d568f5ff98aca6daa3955015d91b6d02766d306f
NeedsCompilation: no
Packaged: 2025-11-11 15:05:31 UTC; root
Author: Katharina Imkeller [cre, aut]
Maintainer: Katharina Imkeller <ag.imkeller@gmail.com>
Built: R 4.5.2; ; 2025-11-11 15:07:34 UTC; windows
