ArticleiMeta2022
iNAP: An integrated network analysis pipeline for microbiome studies.
Article in iMeta, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 1 of them a synthesis that pooled it.
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Who cites it
128 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes.Scientific reports · 2022Pooled it
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- Distinct filtering processes shape bacterial and fungal communities and their co-occurrence patterns across garlic-associated compartments.Environmental microbiome · 2026Article
- MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.BMC bioinformatics · 2026Article
- Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.Microbiome · 2026Article
- Heterogeneous responses of soil microbial communities and functions in coastal wetlands to long-term nitrogen deposition.NPJ biofilms and microbiomes · 2026Article
- Predator-driven microbial feedback loops promote plant health.Nature communications · 2026Article
- Succession of Cyanobacterial Community Contributes to Bacterial and Fungal Community Assembly in Dryland Biocrusts.Ecology and evolution · 2026Article
- Tree Species Mixing Regulates Soil Multi-Nutrient Cycling by Altering Microbial Network Complexity and Assembly Processes inMicroorganisms · 2026Article
- Bacterial co-detection is associated with higher multidrug-resistantJAC-antimicrobial resistance · 2026Article
- Bacteroides thetaiotaomicron: A symbiotic ally against diarrhea along with modulation of gut microbial ecological networks via tryptophan metabolism and AHR-Nrf2 signaling.Journal of advanced research · 2026Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integrated network analysis pipeline (iNAP) is an online analysis pipeline for generating and analyzing comprehensive ecological networks in microbiome studies. It is implemented in two sections, that is, network construction and network analysis, and integrates many open-access tools. Network construction contains multiple feasible alternatives, including correlation-based approaches (Pearson's correlation and Spearman's rank correlation along with random matrix theory, and sparse correlations for compositional data) and conditional dependence-based methods (extended local similarity analysis and sparse inverse covariance estimation for ecological association inference), while network analysis provides topological structures at different levels and the potential effects of environmental factors on network structures. Considering the full workflow, from microbiome data set to network result, iNAP contains the molecular ecological network analysis pipeline and interdomain ecological network analysis pipeline (IDENAP), which correspond to the intradomain and interdomain associations of microbial species at multiple taxonomic levels. Here, we describe the detailed workflow by taking IDENAP as an example and show the comprehensive steps to assist researchers to conduct the relevant analyses using their own data sets. Afterwards, some auxiliary tools facilitating the pipeline are introduced to effectively aid in the switch from local analysis to online operations. Therefore, iNAP, as an easy-to-use platform that provides multiple network-associated tools and approaches, can enable researchers to better understand the organization of microbial communities. iNAP is available at http://mem.rcees.ac.cn:8081 with free registration.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.