R Observatory: Metrics for scDiffCom version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scDiffCom

1.2.0

Differential Analysis of Intercellular Communication from scRNA-Seq Data

0packages depend

4.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Cyril LaggerFirst published 2021-08-173 releasesCRAN page ↗GitHub ↗

Analysis tools to investigate changes in intercellular communication from scRNA-seq data. Using a Seurat object as input, the package infers which cell-cell interactions are present in the dataset and how these interactions change between two conditions of interest (e.g. young vs old). It relies on an internal database of ligand-receptor interactions (available for human, mouse and rat) that have been gathered from several published studies. Detection and differential analyses rely on permutation tests. The package also contains several tools to perform over-representation analysis and visualize the results. See Lagger, C. et al. (2023) doi:10.1038/s43587-023-00514-x for a full description of the methodology.

Install

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

install.packages("scDiffCom", 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("CyrilLagger/scDiffCom")

Development version from CyrilLagger/scDiffCom. 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-scdiffcom

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: 10.0 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.12

not tracked

Coverage

100%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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
WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 137 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 98%
Return-value docs: 100%
References docs: 26%

Downloads

4.2K

CRAN downloads in the past year

Rank #11,168 · ~11/day · ~347/mo

Releases R versions

Daily download trend is not available in this view yet.

26430 days

87290 days

4.2K1 year

Compare downloads with other packages →

Also on199 r2u

Repository

GitHub ↗ cyrillagger/scdiffcom

25Stars

1Forks

1Open issues

0Open PRs

0Releases

477Commits

3Contributors

477 commits · Last activity 2025-10-14 · 0% stars, 30d

Stars over time

2025-08-13 · 222026-07-07 · 25

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/cyrillagger/scdiffcom on 2026-08-16.

Continuous integration (2)

GitHub ActionsTravis CI

Reproducibility and dev environment (2)

renvdata-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

29 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (10)

data.table DelayedArray future future.apply lifecycle magrittrmethodsSeuratstatsutils

LinkingTo (0)

none

Suggests (22)

biomaRt covr DT ggplot2 GOSemSim igraph kableExtra KEGGREST knitr ontologyIndex ontoProc pkgdown plotly RColorBrewer rmarkdown rrvgo spelling shiny shinythemes shinyWidgets testthat visNetwork

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Cyril Lagger

Author, Maintainer

Authors (2)

Cyril Lagger

Author, Maintainer

Eugen Ursu

Author

Contributors (1)

Anais Equey

Contributor

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
1.2.0Latest
2025-10-14 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.0
2023-11-03 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.0
2021-08-17
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-08-17
Total releases: 3 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 1.9 MB / 5 files
Download size: 2.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scDiffCom")

Format

Lagger, C., Equey, A., & Ursu, E. (2025). scDiffCom: Differential Analysis of Intercellular Communication from scRNA-Seq Data (Version 1.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.scDiffCom

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 scDiffCom version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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