R Observatory: Metrics for ogrdbstats version 0.5.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ogrdbstats

0.5.5

Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics

0packages depend

2.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by William LeesFirst published 2023-03-094 releasesCRAN page ↗GitHub ↗

Multiple tools are now available for inferring the personalised germ line set from an adaptive immune receptor repertoire. Output from these tools is converted to a single format and supplemented with rich data such as usage and characterisation of 'novel' germ line alleles. This data can be particularly useful when considering the validity of novel inferences. Use of the analysis provided is described in doi:10.3389/fimmu.2019.00435.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("ogrdbstats", 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("airr-community/ogrdbstats")

Development version from airr-community/ogrdbstats. 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-ogrdbstats

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

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

16

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-28
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-07-27
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-24
10 OK · 0 NOTE · 3 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-03-10
11 OK · 0 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.8K

CRAN downloads in the past year

Rank #18,641 · ~8/day · ~232/mo

Releases R versions

Daily download trend is not available in this view yet.

18030 days

58590 days

2.8K1 year

Compare downloads with other packages →

Also on111 r2u

Repository

GitHub ↗ airr-community/ogrdbstats

1Stars

0Forks

0Open issues

0Open PRs

1Releases

103Commits

1Contributors

103 commits · Last activity 2026-08-03

Stars over time

2023-03-17 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/airr-community/ogrdbstats on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Dockerfile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4

Imports (16)

dplyr ggplot2 magrittr tigger (>= 0.4.0)alakazam stringr data.table gridExtra tidyr stringdist RColorBrewer pwalign argparser (>= 0.4)ComplexHeatmap bookdown scales

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 (1)

Maintainer (1)

William Lees

Author, Maintainer

Authors (1)

William Lees

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.5.5Latest
2026-03-23 · current release · diff ↗
0.5.4
2025-07-08 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.5.2
2024-11-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.5.0
2023-03-09
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-03-09
Total releases: 4 / 3 yrs
License: CC BY-SA 4.0
Additional repositories: bioconductor.org
Minimum R: ≥ 4.4
Bundled data: 12 KB / 1 file
Download size: 116 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ogrdbstats")

Format

Lees, W. (2026). ogrdbstats: Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics (Version 0.5.5) [Computer software]. https://doi.org/10.32614/CRAN.package.ogrdbstats

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ogrdbstats version 0.5.5 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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