hlaR

1.0.0

Tools for HLA Data

0packages depend

2.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Joan ZhangFirst published 2021-04-138 releasesCRAN page ↗GitHub ↗

A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database https://haplostats.org/haplostats. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' http://www.epitopes.net versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("hlaR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("LarsenLab/hlaR")

Development version from LarsenLab/hlaR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-hlar

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-hlaR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-hlaR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.8K

CRAN downloads in the past year

Rank #14,933 · ~8/day · ~229/mo

Releases R versions

Daily download trend is not available in this view yet.

21130 days

74790 days

2.8K1 year

Compare downloads with other packages →

Also on91 r2u37 autocran

Repository

GitHub ↗ larsenlab/hlar

9Stars

3Forks

0Open issues

1Open PRs

0Releases

509Commits

3Contributors

509 commits · Last activity 2023-03-02

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/larsenlab/hlar on 2026-07-19.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (13)

devtools tidyverse dplyr reshape2 schoolmath tibble tidyselect stringr purrr tidyrutilsreadr janitor

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Joan Zhang

Author, Maintainer

Authors (3)

Joan Zhang

Author, Maintainer

Aileen Johnson

Author

Christian P Larsen

Package Timeline

8 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.0Latest
2023-01-31 · current release · diff ↗
0.1.6
2022-12-21 · diff ↗
0.1.5
2022-10-24 · diff ↗
0.1.4
2022-09-12 · diff ↗
0.1.3
2022-05-13 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.2
2022-02-01 · diff ↗
0.1.1
2021-09-27 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.0
2021-04-13
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-04-13
Total releases: 8 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 112 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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