iNAP: An integrated network analysis pipeline for microbiome studies
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. Netw...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-06-01
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| Series: | iMeta |
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| Online Access: | https://doi.org/10.1002/imt2.13 |
| _version_ | 1828141399022764032 |
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| author | Kai Feng Xi Peng Zheng Zhang Songsong Gu Qing He Wenli Shen Zhujun Wang Danrui Wang Qiulong Hu Yan Li Shang Wang Ye Deng |
| author_facet | Kai Feng Xi Peng Zheng Zhang Songsong Gu Qing He Wenli Shen Zhujun Wang Danrui Wang Qiulong Hu Yan Li Shang Wang Ye Deng |
| author_sort | Kai Feng |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T19:25:14Z |
| format | Article |
| id | doaj.art-51dd45d6dbea423a8ff1a358176e05f0 |
| institution | Directory Open Access Journal |
| issn | 2770-596X |
| language | English |
| last_indexed | 2024-04-11T19:25:14Z |
| publishDate | 2022-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | iMeta |
| spelling | doaj.art-51dd45d6dbea423a8ff1a358176e05f02022-12-22T04:07:11ZengWileyiMeta2770-596X2022-06-0112n/an/a10.1002/imt2.13iNAP: An integrated network analysis pipeline for microbiome studiesKai Feng0Xi Peng1Zheng Zhang2Songsong Gu3Qing He4Wenli Shen5Zhujun Wang6Danrui Wang7Qiulong Hu8Yan Li9Shang Wang10Ye Deng11CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing ChinaCAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing ChinaInstitute for Marine Science and Technology Shandong University Qingdao ChinaCAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing ChinaCAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing ChinaInstitute for Marine Science and Technology Shandong University Qingdao ChinaCAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing ChinaCAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing ChinaCollege of Horticulture Hunan Agricultural University Changsha ChinaWest China Hospital of Stomatology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases Sichuan University Chengdu ChinaCAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing ChinaCAS Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing ChinaAbstract 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.https://doi.org/10.1002/imt2.13interactionmicrobial associationmicrobiomenetwork analyses |
| spellingShingle | 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 interaction microbial association microbiome network analyses |
| title | iNAP: An integrated network analysis pipeline for microbiome studies |
| title_full | iNAP: An integrated network analysis pipeline for microbiome studies |
| title_fullStr | iNAP: An integrated network analysis pipeline for microbiome studies |
| title_full_unstemmed | iNAP: An integrated network analysis pipeline for microbiome studies |
| title_short | iNAP: An integrated network analysis pipeline for microbiome studies |
| title_sort | inap an integrated network analysis pipeline for microbiome studies |
| topic | interaction microbial association microbiome network analyses |
| url | https://doi.org/10.1002/imt2.13 |
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