R Observatory: Metrics for CytOpT version 0.9.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CytOpT

0.9.8

Optimal Transport for Gating Transfer in Cytometry Data with Domain Adaptation

0packages depend

3.1Kdownloads / year

38.8%test coverage

13/13checks pass

Overview

About

Maintained by Boris HejblumFirst published 2022-02-075 releasesCRAN page ↗GitHub ↗

Supervised learning from a source distribution (with known segmentation into cell sub-populations) to fit a target distribution with unknown segmentation. It relies regularized optimal transport to directly estimate the different cell population proportions from a biological sample characterized with flow cytometry measurements. It is based on the regularized Wasserstein metric to compare cytometry measurements from different samples, thus accounting for possible mis-alignment of a given cell population across sample (due to technical variability from the technology of measurements). Supervised learning technique based on the Wasserstein metric that is used to estimate an optimal re-weighting of class proportions in a mixture model Details are presented in Freulon P, Bigot J and Hejblum BP (2023) doi:10.1214/22-AOAS1660.

Install

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

install.packages("CytOpT", 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("sistm/CytOpT-R")

Development version from sistm/CytOpT-R. 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-cytopt

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-CytOpT

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-CytOpT

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

Health

CRAN checks

13OK

Slowest check: 4.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

38.8%

Coverage · measured lines

100%

Documentation · exports

7

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 221 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 86%
References docs: 8%

Downloads

3.1K

CRAN downloads in the past year

Rank #12,233 · ~9/day · ~259/mo

Releases R versions

Daily download trend is not available in this view yet.

23930 days

82690 days

3.1K1 year

Compare downloads with other packages →

Also on147 r2u18 autocran

Repository

GitHub ↗ sistm/cytopt-r

1Stars

0Forks

0Open issues

0Open PRs

2Releases

164Commits

2Contributors

License GPL-2.0 · 164 commits · Last activity 2025-04-04

Stars over time

2022-04-07 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/sistm/cytopt-r on 2026-08-09.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6

Imports (7)

ggplot2 MetBrewer patchwork reshape2 reticulatestatstestthat

LinkingTo (0)

none

Suggests (3)

rmarkdown knitr covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Boris Hejblum

Author, Maintainer

Authors (3)

Boris Hejblum

Author, Maintainer

Kalidou Ba

Author, Translator

Paul Freulon

Author

Translators (1)

Kalidou Ba

Author, Translator

Package Timeline

5 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
0.9.8Latest
2025-04-01 · current release · diff ↗
unarchivedReturned to CRAN
2025-04-01
archivedRemoved from CRAN
2025-03-31
repeated policy violation
0.9.7
2025-03-30 · diff ↗
unarchivedReturned to CRAN
2025-03-30
archivedRemoved from CRAN
2025-03-28
policy violation Averaging ca 4 cores, even after update
0.9.6
2025-03-26 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.9.4
2022-02-09 · diff ↗
0.9.2
2022-02-07
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-02-07
Total releases: 5 / 4 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.6
Bundled data: 1.4 MB / 1 file
Download size: 2.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CytOpT")

Format

Hejblum, B., Ba, K., & Freulon, P. (2025). CytOpT: Optimal Transport for Gating Transfer in Cytometry Data with Domain Adaptation (Version 0.9.8) [Computer software]. https://doi.org/10.32614/CRAN.package.CytOpT

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 CytOpT version 0.9.8 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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