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immunotation

Tools for working with diverse immune genes


Bioconductor version: Release (3.18)

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.

Author: Katharina Imkeller [cre, aut]

Maintainer: Katharina Imkeller <k.imkeller at dkfz.de>

Citation (from within R, enter citation("immunotation")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("immunotation")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("immunotation")
User guide immunotation HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, BiomedicalInformatics, Genetics, ImmunoOncology, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.1)
Imports stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr, xml2, maps, rlang
System Requirements
URL
Bug Reports https://github.com/imkeller/immunotation/issues
See More
Suggests BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package immunotation_1.10.0.tar.gz
Windows Binary immunotation_1.10.0.zip
macOS Binary (x86_64) immunotation_1.10.0.tgz
macOS Binary (arm64) immunotation_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/immunotation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/immunotation
Bioc Package Browser https://code.bioconductor.org/browse/immunotation/
Package Short Url https://bioconductor.org/packages/immunotation/
Package Downloads Report Download Stats