Package: immunogenetr 1.5.0

immunogenetr: A Comprehensive Toolkit for Clinical HLA Informatics

A comprehensive toolkit for clinical Human Leukocyte Antigen (HLA) informatics, built on 'tidyverse' <https://tidyverse.tidyverse.org/> principles and making use of Genotype List String (GL String, Mack et al. (2023) <doi:10.1111/tan.15126>) for storing and computing HLA genotype data. Specific functionalities include: coercion of HLA data in tabular format to and from GL String; calculation of matching and mismatching in all directions, with multiple output formats; automatic formatting of HLA data for searching within a GL String; truncation of molecular HLA data to a specific number of fields; and reading HLA genotypes in HML files and extracting the GL String. This library is intended for research use. Any application making use of this package in a clinical setting will need to be independently validated according to local regulations.

Authors:Nicholas Brown [cre, aut], Busra Coskun [aut]

immunogenetr_1.5.0.tar.gz
immunogenetr_1.5.0.zip(r-4.7-any)immunogenetr_1.5.0.zip(r-4.6-any)immunogenetr_1.5.0.zip(r-4.5-any)
immunogenetr_1.5.0.tgz(r-4.6-any)immunogenetr_1.5.0.tgz(r-4.5-any)
immunogenetr_1.5.0.tar.gz(r-4.7-any)immunogenetr_1.5.0.tar.gz(r-4.6-any)
immunogenetr_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
immunogenetr/json (API)

# Install 'immunogenetr' in R:

install.packages('immunogenetr', repos = c('https://k96nb01.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/k96nb01/immunogenetr_package/issues

Pkgdown/docs site:https://immunogenetr.org

Datasets:

Haplotype_frequencies - Ten HLA-A~C~B~DRB3/4/5~DRB1~DQA1~DQB1~DPA1~DPB1 haplotypes and their frequencies in the global population.
HLA_dictionary - Data on HLA alleles in the 2008 HLA dictionary
HLA_typing_1 - Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3/4/5, DQB1, DQA1, DPB1 and DPA1 loci.
HLA_typing_LIS - Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQB1, DQA1, DPB1 and DPA1 loci. Data formatted to resemble a HistoTrac table.
HLA_typing_synthetic_LIS - Synthetic clinical-laboratory HLA typing table (HistoTrac "Patient" layout).
mismatch_table_2010 - Consensus mismatch numbers for every possible allele combination at a single locus, from the 2010 publication.
mismatch_table_2016 - Consensus mismatch numbers for every possible allele combination at a single locus, from the 2016 publication.

On CRAN:

hla hla-typing informatics tidyverse

5.88 score 6 stars 25 scripts 252 downloads 23 exports 21 dependencies

Last updated from:2b8c52ccad. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	144
source / vignettes	OK	250
linux-release	OK	163
macos-release	OK	88
macos-oldrel	OK	105
windows-devel	OK	98
windows-release	OK	78
windows-oldrel	OK	95
wasm-release	OK	114

Exports:ambiguity_table_to_GLstring GLstring_drop_non_expressed GLstring_expand_longer GLstring_gene_copies_combine GLstring_genes GLstring_genes_expanded GLstring_genotype_ambiguity GLstring_regex GLstring_to_ambiguity_table HLA_column_repair HLA_columns_to_GLstring HLA_match_number HLA_match_summary_HCT HLA_mismatch_alleles HLA_mismatch_base HLA_mismatch_logical HLA_mismatch_number HLA_mismatched_alleles HLA_prefix_add HLA_prefix_remove HLA_truncate HLA_validate read_HML

Dependencies:cli cpp11 dplyr generics glue lifecycle magrittr pillar pkgconfig purrr R6 rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr xml2

Getting Started with immunogenetr

Rendered fromimmunogenetr.Rmdusingknitr::rmarkdown

Last update: 2026-08-16
Started: 2026-04-06

Help page	Topics
ambiguity_table_to_GLstring	ambiguity_table_to_GLstring
GLstring_drop_non_expressed	GLstring_drop_non_expressed
GLstring_expand_longer	GLstring_expand_longer
GLstring_gene_copies_combine	GLstring_gene_copies_combine
GLstring_genes	GLstring_genes
GLstring_genes_expanded	GLstring_genes_expanded
GLstring_genotype_ambiguity	GLstring_genotype_ambiguity
GLstring_regex	GLstring_regex
GLstring_to_ambiguity_table	GLstring_to_ambiguity_table
Ten HLA-A~C~B~DRB3/4/5~DRB1~DQA1~DQB1~DPA1~DPB1 haplotypes and their frequencies in the global population.	Haplotype_frequencies
HLA_column_repair	HLA_column_repair
HLA_columns_to_GLstring	HLA_columns_to_GLstring
Data on HLA alleles in the 2008 HLA dictionary	HLA_dictionary
HLA_match_number	HLA_match_number
HLA_match_summary_HCT	HLA_match_summary_HCT
HLA_mismatch_alleles	HLA_mismatch_alleles
HLA_mismatch_base	HLA_mismatch_base
HLA_mismatch_logical	HLA_mismatch_logical
HLA_mismatch_number	HLA_mismatch_number
HLA_mismatched_alleles	HLA_mismatched_alleles
HLA_prefix_add	HLA_prefix_add
HLA_prefix_remove	HLA_prefix_remove
HLA_truncate	HLA_truncate
Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3/4/5, DQB1, DQA1, DPB1 and DPA1 loci.	HLA_typing_1
Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQB1, DQA1, DPB1 and DPA1 loci. Data formatted to resemble a HistoTrac table.	HLA_typing_LIS
Synthetic clinical-laboratory HLA typing table (HistoTrac "Patient" layout).	HLA_typing_synthetic_LIS
HLA_validate	HLA_validate
Consensus mismatch numbers for every possible allele combination at a single locus, from the 2010 publication.	mismatch_table_2010
Consensus mismatch numbers for every possible allele combination at a single locus, from the 2016 publication.	mismatch_table_2016
read_HML	read_HML

Package: immunogenetr 1.5.0

immunogenetr: A Comprehensive Toolkit for Clinical HLA Informatics

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