immunotation
This is the development version of immunotation; for the stable release version, see immunotation.
Tools for working with diverse immune genes
Bioconductor version: Development (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("immunotation")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, BiomedicalInformatics, Genetics, ImmunoOncology, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (2 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr, xml2, maps, rlang |
| Linking To | |
| Suggests | BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT |
| System Requirements | |
| Enhances | |
| URL | |
| Bug Reports | https://github.com/imkeller/immunotation/issues |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | immunotation_1.9.0.tar.gz |
| Windows Binary | immunotation_1.9.0.zip |
| macOS Binary (x86_64) | immunotation_1.9.0.tgz |
| macOS Binary (arm64) | immunotation_1.9.0.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 |