ArticleComputational and structural biotechnology journal2022
CommPath: An R package for inference and analysis of pathway-mediated cell-cell communication chain from single-cell transcriptomics.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Multi-omics analysis reveals that CAPG positive macrophages are key immunosuppressive drivers and prognostic determinants in the ferroptosis landscape of hepatocellular carcinoma.Discover oncology · 2026Article
- Single-cell transcriptomics identifies fibroblast associated immune heterogeneity and prognostic signatures in bladder cancer.Scientific reports · 2026Article
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- Development and validation of a prognostic model for predicting survival and immunotherapy benefits in melanoma based on metabolism-relevant genes.Discover oncology · 2025Article
- CausalCCC: a web server to explore intracellular causal pathways enabling cell-cell communication.Nucleic acids research · 2025Article
- CellNEST reveals cell-cell relay networks using attention mechanisms on spatial transcriptomics.Nature methods · 2025Article
- Integrating multi-omics data to identify the role of Aggrephagy-related genes in tumor microenvironment and key tumorigenesis factors of GB from the perspective of single-cell sequencing.Discover oncology · 2025Article
- Development of a prognostic model for osteosarcoma based on macrophage polarization-related genes using machine learning: implications for personalized therapy.Clinical and experimental medicine · 2025Article
- Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions.Briefings in bioinformatics · 2025Review
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- Comprehensive single-cell atlas of colorectal neuroendocrine tumors with liver metastases: unraveling tumor microenvironment heterogeneity between primary lesions and metastases.Molecular cancer · 2025Article
- Comprehensive Analysis of Multi-Omics Data on RNA Polymerase as an Adverse Factor in Head and Neck Squamous Cell Carcinoma.Journal of inflammation research · 2025Article
- The diversification of methods for studying cell-cell interactions and communication.Nature reviews. Genetics · 2024Review
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9 authors.
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Abstract
Single-cell transcriptomics offers opportunities to investigate ligand-receptor (LR) interactions between heterogeneous cell populations within tissues. However, most existing tools for the inference of intercellular communication do not allow prioritization of functional LR associations that provoke certain biological responses in the receiver cells. In addition, current tools do not enable the identification of the impact on the downstream cell types of the receiver cells. We present CommPath, an open-source R package and webserver, to analyze and visualize the LR interactions and pathway-mediated intercellular communication chain with single-cell transcriptomic data. CommPath curates a comprehensive signaling pathway database to interpret the consequences of LR associations and therefore infers functional LR interactions. Furthermore, CommPath determines cell-cell communication chain by considering both the upstream and downstream cells of user-defined cell populations. Applying CommPath to human hepatocellular carcinoma dataset shows its ability to decipher complex LR interaction patterns and the associated intercellular communication chain, as well as their changes in disease versus homeostasis.
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