{"id":29267665,"url":"https://github.com/muellsen/mna","last_synced_at":"2025-10-10T21:10:05.076Z","repository":{"id":89982535,"uuid":"91504438","full_name":"muellsen/MNA","owner":"muellsen","description":" MATLAB scripts and functions for Microbial Network Analysis (MNA)","archived":false,"fork":false,"pushed_at":"2020-02-16T17:12:21.000Z","size":3121,"stargazers_count":2,"open_issues_count":1,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-07-04T18:15:25.416Z","etag":null,"topics":["graphlets","microbial","microbiome","networks"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/muellsen.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-05-16T21:05:28.000Z","updated_at":"2023-03-08T04:18:33.000Z","dependencies_parsed_at":"2023-05-30T19:30:45.401Z","dependency_job_id":null,"html_url":"https://github.com/muellsen/MNA","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/muellsen/MNA","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/muellsen%2FMNA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/muellsen%2FMNA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/muellsen%2FMNA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/muellsen%2FMNA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/muellsen","download_url":"https://codeload.github.com/muellsen/MNA/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/muellsen%2FMNA/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005409,"owners_count":26083883,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-10T02:00:06.843Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["graphlets","microbial","microbiome","networks"],"created_at":"2025-07-04T18:14:57.020Z","updated_at":"2025-10-10T21:10:05.067Z","avatar_url":"https://github.com/muellsen.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Microbial Network Analysis (MNA) in MATLAB\n\n\nThis project comprises a collection of functions and scripts for (microbial) network analysis. This repository is constantly expanded and tested. Many of the scripts have been used in a number of publications.\n\n## Publications that used the MATLAB functions and scripts \n\n* [1] Mahana et al. [Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0297-9), Genome Medicine, vol 8:48 (2016) \n* [2] Ruiz et al., [A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity](https://www.nature.com/articles/s41467-017-00531-6), Nature Communications, vol 8:518 (2017)\n\n* [3] Tipton, Müller, et al. [Fungi stabilize connectivity in the lung and skin microbial ecosystems](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0393-0), Microbiome, vol 6:12 (2018) \n\nThe folder Paper-Ruiz-2017/ comprises results from [2]. The folder Tipton-2018/ comprises results from [3]. Please cite these papers when using (variations of) this code for similar analysis pipelines.\n\n## Graphlets, graphlet correlations, and graphlet correlation distance computation\n\nThe folder GraphletComputation/ shows how to do microbial network comparisons for networks of different sizes. It is based on \nthe Graphlet Correlation Distance (GCD), as introduced in \n* [4] Yaveroglu et al., [Revealing the Hidden Language of Complex Networks](https://www.nature.com/articles/srep04547), Scientific Reports, vol 4:4547 (2014).\n\nFor computation of the graphlets (i.e., small induced subgraphs), the orca package is used, as introduced in\n* [5] Hocevar \u0026 Demsar, [A combinatorial approach to graphlet counting](https://academic.oup.com/bioinformatics/article/30/4/559/205331), Bioinformatics, vol 30:4,559--565 (2014).\nThe github CRAN read-only mirror for the orca package can be found [here.](https://github.com/cran/orca)\n\n* [6] Hocevar \u0026 Demsar, [Computation of graphlet orbits for nodes and edges in sparse graphs](https://www.jstatsoft.org/article/view/v071i10/0), Journal of Statistical Software,  vol 71:10 (2016)\nThe orca homepage with supporting information can be found [here.](http://www.biolab.si/supp/Rorca/) \n\nPlease cite these papers when using (variations of) this code for similar analysis pipelines.\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmuellsen%2Fmna","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmuellsen%2Fmna","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmuellsen%2Fmna/lists"}