TCMNP: a data processing and visualization database and R package for traditional Chinese medicine network pharmacology

BackgroundNetwork pharmacology is pivotal for the study of the mechanism of action of traditional Chinese medicine (TCM). However, there are currently some challenges in data processing and visualization for traditional Chinese medicine network pharmacology (TCMNP). We develop the R-environment-based software database and package TCMNP. MethodsTCMNP is designed for the analysis and visualization of compositions in TCM compounds, herbs, ingredients, corresponding targets and pathway enrichment. Data analysis and visualization in R using "dplyr", "clusterProfiler", "ggplot2", and "circlize" packages, as well as functions of our own making. ResultsTCMNP is designed for the analysis and visualization of compositions in TCM compounds, herbs, ingredients, corresponding targets and pathway. The TCMNP database contains 571 kinds of TCM herbs, 17,118 ingredients, 10,013 diseases, and 15,956 targets. TCMNP simplifies the data analysis process and realizes a complete set of process operations from Chinese herbal compound composition, component and target automatic screening, enrichment analysis visualization, protein interaction and TF and target gene screening. Its built-in functions of various types provide a tidy interface for the visualization of TCM network pharmacology. TCMNP database is freely available at https://tcmlab.top/tcmr. TCMNP package is freely available at https://github.com/tcmlab/TCMNP. ConclusionThe TCMNP database and package provide a comprehensive overview of the interconnections between components of a TCM compound and its potential effects on disease treatment. TCMNP database is available for free at https://tcmlab.top/tcmr/. TCMNP package is available for free at https://github.com/tcmlab/TCMNP. We anticipate that TCMNP will help to explore the mechanism of TCM to treat diseases.