PopComm

1.0.0

Population-Level Cell-Cell Communication Analysis Tools

0packages depend

2.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Zheng GongFirst published 2025-04-252 releasesCRAN page ↗GitHub ↗

Facilitates population-level analysis of ligand-receptor (LR) interactions using large-scale single-cell transcriptomic data. Identifies significant LR pairs and quantifies their interactions through correlation-based filtering and projection score computations. Designed for large-sample single-cell studies, the package employs statistical modeling, including linear regression, to investigate LR relationships between cell types. It provides a systematic framework for understanding cell-cell communication, uncovering regulatory interactions and signaling mechanisms. Offers tools for LR pair-level, sample-level, and differential interaction analyses, with comprehensive visualization support to aid biological interpretation. The methodology is described in a manuscript currently under review and will be referenced here once published or publicly available.

Install

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

install.packages("PopComm", 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("JusticeGO/PopComm")

Development version from JusticeGO/PopComm. 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-popcomm

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-PopComm

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-PopComm

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

Health

CRAN checks

13OK

Slowest check: 3.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 46%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #16,621 · ~7/day · ~199/mo

Releases R versions

Daily download trend is not available in this view yet.

24230 days

66590 days

2.4K1 year

Compare downloads with other packages →

Also on178 r2u18 autocran

Repository

GitHub ↗ justicego/popcomm

1Stars

0Forks

0Open issues

0Open PRs

1Releases

93Commits

1Contributors

License MIT · 93 commits · Last activity 2026-02-04 · 0% stars, 30d

Stars over time

2026-03-01 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

Checks run against github.com/justicego/popcomm on 2026-07-26.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (21)

Seurat broom dplyr purrr rlang stringr tibble tidyr tidyselectMatrixggplot2 ggpubr pheatmap RColorBrewer reshape2 scales igraphparallelpbmcapplygrDevicescowplot

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Zheng Gong

Author, Maintainer

Authors (2)

Zheng Gong

Author, Maintainer

Mengwei Li

Author, Contributor

Contributors (1)

Mengwei Li

Author, 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
1.0.0Latest
2025-11-01 · current release · diff ↗
0.1.0.1
2025-04-25
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-25
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.8 MB / 5 files
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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