R Observatory: Metrics for PopComm version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PopComm

1.0.0Package record

Population-Level Cell-Cell Communication Analysis Tools

0packages depend

2.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Zheng GongCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.0.0

Changes in filter_lr_single(), filter_lr_all(), score_lr_single(), single_lr_all(), one_step_single(), one_step_all()

Added support for average expression matrices. These functions now accept either Seurat objects or average expression matrices (a numeric matrix of gene expression where columns encode cell types and samples, and rows are genes).
No changes to existing Seurat-based workflows.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMENoVignettesNoNEWSYes · 67% structured · mentions 1.0.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 18
Examples that run: 46%6 run in a plain check · 7 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #17,085 · ~7/day · ~215/mo

Releases R versions

Daily download trend is not available in this view yet.

29630 days

73990 days

2.6K1 year

Compare downloads with other packages →

Also on109 r2u1 autocran

How downloads are counted

Repository

justicego/popcomm ↗Account: JusticeGO

1Stars

0Forks

0Open issues

0Open PRs

1Releases

93Commits

1Commit identities

License file reads as MIT · 93 commits · Last activity 2026-02-04 · 0% stars, 30d · Default branch at 1.0.1, ahead of CRAN 1.0.0 (checked 2026-10-18)

Responsiveness

not measured

Stars over time

2026-03-01 · 12026-07-07 · 1

How these are measured

PracticesBeta

Checks run against github.com/justicego/popcomm on 2026-10-18.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing PopComm adds 167 packages (94 with compiled code, 155 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Zheng Gong

Author, Maintainer since 0.1.0.1 (2025)

Mengwei Li

Author, Contributor

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
record
2025-11-01 · current release · diff ↗ ·
removed 1 export
load_example_seurat
0.1.0.1
record
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

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PopComm")

Format

Gong, Z., & Li, M. (2025). PopComm: Population-Level Cell-Cell Communication Analysis Tools (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PopComm

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 PopComm version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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