Welcome to iNAP (integrated Network Analysis Pipeline) for microbiome studies!

---

This analysis pipeline is built and maintained by Metagenomics for Environmental Microbiology (MEM) (DengLab), led by Prof. Ye Deng. It is used to model, analyze and manage the the Molecular Ecological Networks (MENs) for adjacent matrix and Inter-Domain Ecological Networks (IDENs) for bipartite matrix from metagenomic datasets, e.g. GeoChip and Sequencing, and synchronous plant surveys, including Molecular Ecological Network Analysis (MENA) Pipeline and InterDomain Ecological Network Analysis Pipeline (IDENAP).

Currently, we integrated several publicly approaches for network construction, including RMT-based MENA (Random Matrix Theory), SparCC (Sparse Correlations for Compositional data), eLSA (extended Local Similarity Analysis) and SPIEC-EASI (Sparse InversE Covariance estimation for Ecological Association and Statistical Inference). For other methods or approaches, we will also include them if possible and please email us.

Please see the workflow below and download the procedure file for more details.

Please cite: Kai Feng, Xi Peng, Zheng Zhang, Songsong Gu, Qing He, Wenli Shen, Zhujun Wang, Danrui Wang, Qiulong Hu, Yan Li, Shang Wang, Ye Deng. iNAP: an integrated Network Analysis Pipeline for microbiome studies. iMeta. 2022,1:e13. https://doi.org/10.1002/imt2.13

See also: Kai Feng, Yuguang Zhang, Zhili He, Daliang Ning, Ye Deng. Interdomain ecological networks between plants and microbes. Molecular Ecology Resources. 2019,19 (6):1565-1577. doi:10.1111/1755-0998.13081

Metabolic Modeling Analysis is now online for everyone to use. The workflow instructions: iNAP2 Instructions For details, See and cite: Xi Peng, Kai Feng, Xingsheng Yang, Qing He, Bo Zhao, Tong Li, Shang Wang, and Ye Deng. 2024. “ iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis.” iMeta. e235. https://doi.org/10.1002/imt2.235

A sample study using the metabolic modeling analysis pipeline: Peng, X., Wang, S., Wang, M. et al. Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks. Nat Commun 15, 8166 (2024).https://doi.org/10.1038/s41467-024-52532-x

The pipeline is freely open for publics to register and please only use this for academic researches. Since there is limited running time and process for anonymous accout, we suggest to run the pipeline with registered account, including your username, emails and affiliations. If you are interested in our analysis approach, please feel free to contact with Prof. Ye Deng (yedeng@rcees.ac.cn).

We are now making it mandatory for new users to use a strong password (both upper and lower case letters and numbers) when signing up for an account, and we recommend that all users change their password to one that matches these requirements.