cytometree

2.0.6

Automated Cytometry Gating and Annotation

0packages depend

4.1Kdownloads / year

3.8%test coverage

12/13checks pass

Overview

About

Maintained by Boris P HejblumFirst published 2017-06-268 releasesCRAN page ↗GitHub ↗

Given the hypothesis of a bi-modal distribution of cells for each marker, the algorithm constructs a binary tree, the nodes of which are subpopulations of cells. At each node, observed cells and markers are modeled by both a family of normal distributions and a family of bi-modal normal mixture distributions. Splitting is done according to a normalized difference of AIC between the two families. Method is detailed in: Commenges, Alkhassim, Gottardo, Hejblum & Thiebaut (2018) <doi: 10.1002/cyto.a.23601>.

Install

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

install.packages("cytometree", 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/Cytometree")

Development version from sistm/Cytometree. 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-cytometree

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-cytometree

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-cytometree

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 12.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.01

3.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 233 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 50%
References docs: 7%

Downloads

4.1K

CRAN downloads in the past year

Rank #11,011 · ~11/day · ~344/mo

Releases R versions

Daily download trend is not available in this view yet.

29930 days

92590 days

4.1K1 year

Compare downloads with other packages →

Also on447 r2u5 autocran2.4K conda_forge

Repository

GitHub ↗ sistm/cytometree

11Stars

6Forks

1Open issues

0Open PRs

0Releases

218Commits

5Contributors

218 commits · Last activity 2025-07-26 · +10% stars, 30d

Stars over time

2025-07-28 · 92026-07-07 · 11

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/sistm/cytometree on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Coverage (1)

Codecov

Show all practices

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.1.0Rcpp

Imports (8)

ggplot2graphicsigraph mclustmethodsstatscowplot GoFKernel

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (5)

knitr formatR rmarkdown viridis testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Boris P Hejblum

Maintainer, Author · added in 2.0.2

Authors (5)

Boris P Hejblum

Maintainer, Author · added in 2.0.2

Chariff Alkhassim

Author · added in 1.1.1

Anthony Devaux

Author · added in 1.2.0

Melany Durand

Author · added in 2.0.6

Van Hung Huynh Tran

Author · added in 1.3.0

Listed in earlier versions (1)

Boris Hejblum

no longer listed · 1.1.1 to 2.0.0

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
2.0.6Latest
2025-07-24 · current release · diff ↗
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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.0.2
2019-12-04 · diff ↗
2.0.0
2019-08-19 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.3.0
2019-01-12 · diff ↗
1.2.0
2018-08-28 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.1.1
2017-10-22 · diff ↗
1.0.1
2017-07-03 · diff ↗

Show 2 earlier events

1.0.0
2017-06-26
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-06-26
Total releases: 8 / 9 yrs
License: LGPL-3 | file LICENSE OSI
Minimum R: ≥ 3.1.0
Bundled data: 1.6 MB / 3 files
Download size: 2.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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