ggClusterNet 2: An R package for microbial co‐occurrence networks and associated indicator correlation patterns DOI Creative Commons
Tao Wen, Yongxin Liu, Lanlan Liu

et al.

iMeta, Journal Year: 2025, Volume and Issue: unknown

Published: April 25, 2025

Abstract Since its initial release in 2022, ggClusterNet has become a vital tool for microbiome research, enabling microbial co‐occurrence network analysis and visualization over 300 studies. To address emerging challenges, including multi‐factor experimental designs, multi‐treatment conditions, multi‐omics data, we present comprehensive upgrade with four key components: (1) A pipeline integrating computation (Pearson/Spearman/SparCC correlations), visualization, topological characterization of node properties, multi‐network comparison statistical testing, stability (robustness) analysis, module identification analysis; (2) Network mining functions multi‐factor, multi‐treatment, spatiotemporal‐scale Facet.Network() module.compare.m.ts() ; (3) Transkingdom construction using microbiota, multi‐omics, other relevant diverse layouts such as MatCorPlot2() cor_link3() (4) corBionetwork.st() algorithms tailored complex exploration, model_maptree2() , model_Gephi.3() cir.squ() . The updates 2 enable researchers to explore interactions, offering robust, efficient, user‐friendly, reproducible, visually versatile networks indicator correlation patterns. R package is open‐source available on GitHub ( https://github.com/taowenmicro/ggClusterNet ).

Language: Английский

Microbial resistance in agricultural subsoils DOI
Cameron Wagg, Tandra D. Fraser

Nature Food, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Citations

0
Paddy soil fertility shifts microbial metabolic quotient by regulating the selective enrichment of specific bacterial groups DOI Creative Commons

Yali Kong,

Jie Wang, Chunquan Zhu

et al.

Geoderma, Journal Year: 2025, Volume and Issue: 457, P. 117303 - 117303

Published: April 20, 2025

Language: Английский

Citations

0
The fate and ecological risk of typical diamide insecticides in soil ecosystems under repeated application DOI
Xin Zhang, Tong Liu, Wei Sun

et al.

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: unknown, P. 138440 - 138440

Published: April 1, 2025

Language: Английский

Citations

0
ggClusterNet 2: An R package for microbial co‐occurrence networks and associated indicator correlation patterns DOI Creative Commons
Tao Wen, Yongxin Liu, Lanlan Liu

et al.

iMeta, Journal Year: 2025, Volume and Issue: unknown

Published: April 25, 2025

Abstract Since its initial release in 2022, ggClusterNet has become a vital tool for microbiome research, enabling microbial co‐occurrence network analysis and visualization over 300 studies. To address emerging challenges, including multi‐factor experimental designs, multi‐treatment conditions, multi‐omics data, we present comprehensive upgrade with four key components: (1) A pipeline integrating computation (Pearson/Spearman/SparCC correlations), visualization, topological characterization of node properties, multi‐network comparison statistical testing, stability (robustness) analysis, module identification analysis; (2) Network mining functions multi‐factor, multi‐treatment, spatiotemporal‐scale Facet.Network() module.compare.m.ts() ; (3) Transkingdom construction using microbiota, multi‐omics, other relevant diverse layouts such as MatCorPlot2() cor_link3() (4) corBionetwork.st() algorithms tailored complex exploration, model_maptree2() , model_Gephi.3() cir.squ() . The updates 2 enable researchers to explore interactions, offering robust, efficient, user‐friendly, reproducible, visually versatile networks indicator correlation patterns. R package is open‐source available on GitHub ( https://github.com/taowenmicro/ggClusterNet ).

Language: Английский

Citations

0