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PopComm: Population-Level Cell-Cell Communication Analysis Tools

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.

Version: 0.1.0.1
Depends: R (≥ 4.1.0)
Imports: Seurat (≥ 4.1.0), broom (≥ 1.0.0), dplyr (≥ 1.0.0), purrr (≥ 0.3.0), rlang, stringr (≥ 1.4.0), tibble (≥ 3.0.0), tidyr (≥ 1.0.0), tidyselect (≥ 1.1.0), Matrix (≥ 1.2-0), ggplot2 (≥ 3.3.0), ggpubr (≥ 0.6.0), pheatmap (≥ 1.0.12), RColorBrewer, reshape2 (≥ 1.4.1), scales (≥ 1.1.1), igraph (≥ 2.0.0), parallel, pbmcapply (≥ 1.5.0), grDevices
Published: 2025-04-25
DOI: 10.32614/CRAN.package.PopComm
Author: Zheng Gong ORCID iD [aut, cre], Mengwei Li ORCID iD [aut, ctb]
Maintainer: Zheng Gong <gongzheng131 at hotmail.com>
License: MIT + file LICENSE
NeedsCompilation: no
Materials: README
CRAN checks: PopComm results

Documentation:

Reference manual: PopComm.pdf

Downloads:

Package source: PopComm_0.1.0.1.tar.gz
Windows binaries: r-devel: not available, r-release: PopComm_0.1.0.1.zip, r-oldrel: PopComm_0.1.0.1.zip
macOS binaries: r-release (arm64): PopComm_0.1.0.1.tgz, r-oldrel (arm64): PopComm_0.1.0.1.tgz, r-release (x86_64): PopComm_0.1.0.1.tgz, r-oldrel (x86_64): PopComm_0.1.0.1.tgz

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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