R Observatory: Metrics for AntibodyForests version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AntibodyForests

1.1.0

Delineating Inter- And Intra-Antibody Repertoire Evolution

0packages depend

2.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Daphne van GinnekenFirst published 2025-01-232 releasesCRAN page ↗

The generated wealth of immune repertoire sequencing data requires software to investigate and quantify inter- and intra-antibody repertoire evolution to uncover how B cells evolve during immune responses. Here, we present 'AntibodyForests', a software to investigate and quantify inter- and intra-antibody repertoire evolution.

Install

R (CRAN)Ubuntu (r2u)

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

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

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-antibodyforests

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: 3.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

19

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 263 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #12,644 · ~8/day · ~229/mo

Releases R versions

Daily download trend is not available in this view yet.

25630 days

78990 days

2.7K1 year

Compare downloads with other packages →

Also on136 r2u

Dependencies

Declared dependencies

35 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (19)

ape Biostrings dplyrgraphicsgrDevicesgtools igraph magrittrparallelpwalign rlang scales seqinrstatsstringdist stringr tidyrutilsviridis

LinkingTo (0)

none

Suggests (21)

alakazam base64enc bio3d combinat devtools DT fpc ggplot2 ggrepel ggsignif htmltools knitr msa phangorn pheatmap philentropy Peptides Rcompadre rmarkdown RPANDA swipeR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Daphne van Ginneken

Author, Maintainer

Authors (3)

Daphne van Ginneken

Author, Maintainer

Valentijn Tromp

Author

Alexander Yermanos

Author

Contributors (1)

Tudor-Stefan Cotet

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
2025-07-17 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
2025-01-23
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-23
Total releases: 2 / 1 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.0.0
Bundled data: 229 KB / 7 files
Download size: 2.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("AntibodyForests")

Format

van Ginneken, D., Cotet, T., Tromp, V., & Yermanos, A. (2025). AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.AntibodyForests

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 AntibodyForests version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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