cytominer

0.2.2

Methods for Image-Based Cell Profiling

0packages depend

4Kdownloads / year

99.5%test coverage

12/13checks pass

Overview

About

Maintained by Shantanu SinghFirst published 2017-09-173 releasesCRAN page ↗GitHub ↗

Typical morphological profiling datasets have millions of cells and hundreds of features per cell. When working with this data, you must clean the data, normalize the features to make them comparable across experiments, transform the features, select features based on their quality, and aggregate the single-cell data, if needed. 'cytominer' makes these steps fast and easy. Methods used in practice in the field are discussed in Caicedo (2017) doi:10.1038/nmeth.4397. An overview of the field is presented in Caicedo (2016) doi:10.1016/j.copbio.2016.04.003.

Install

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

install.packages("cytominer", 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("cytomining/cytominer")

Development version from cytomining/cytominer. 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-cytominer

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-cytominer

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-cytominer

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: 2.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.06

99.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 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
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 136 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

CRAN downloads in the past year

Rank #14,659 · ~11/day · ~337/mo

Releases R versions

Daily download trend is not available in this view yet.

20430 days

70890 days

4K1 year

Compare downloads with other packages →

Also on108 r2u1 autocran

Repository

GitHub ↗ cytomining/cytominer

52Stars

28Forks

6Open issues

1Open PRs

3Releases

445Commits

9Contributors

profilingmicroscopyr

445 commits · Last activity 2024-05-08 · 0% stars, 30d

Stars over time

2025-05-02 · 512026-07-07 · 52

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/cytomining/cytominer on 2026-08-02.

Continuous integration (1)

Travis CI

Reproducibility and dev environment (1)

renv

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (11)

caret doParallel dplyr foreach futile.logger magrittr (>= 1.5)Matrixpurrr rlang tibble tidyr

LinkingTo (0)

none

Suggests (9)

DBI dbplyr knitr lazyeval readr rmarkdown RSQLite (>= 2.0)stringr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Shantanu Singh

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

Package Timeline

3 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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.2.2Latest
2020-05-09 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
0.2.1
2020-03-23 · diff ↗
unarchivedReturned to CRAN
2020-03-23
archivedRemoved from CRAN
2019-05-08
check problems were not corrected in time
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.1.0
2017-09-17
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-09-17
Total releases: 3 / 9 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.3.0
Download size: 429 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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