https://github.com/muellsen/mna
MATLAB scripts and functions for Microbial Network Analysis (MNA)
https://github.com/muellsen/mna
graphlets microbial microbiome networks
Last synced: 8 months ago
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MATLAB scripts and functions for Microbial Network Analysis (MNA)
- Host: GitHub
- URL: https://github.com/muellsen/mna
- Owner: muellsen
- License: gpl-3.0
- Created: 2017-05-16T21:05:28.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2020-02-16T17:12:21.000Z (over 6 years ago)
- Last Synced: 2025-07-04T18:15:25.416Z (11 months ago)
- Topics: graphlets, microbial, microbiome, networks
- Language: C++
- Homepage:
- Size: 2.98 MB
- Stars: 2
- Watchers: 2
- Forks: 2
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Microbial Network Analysis (MNA) in MATLAB
This 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.
## Publications that used the MATLAB functions and scripts
* [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)
* [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)
* [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)
The 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.
## Graphlets, graphlet correlations, and graphlet correlation distance computation
The folder GraphletComputation/ shows how to do microbial network comparisons for networks of different sizes. It is based on
the Graphlet Correlation Distance (GCD), as introduced in
* [4] Yaveroglu et al., [Revealing the Hidden Language of Complex Networks](https://www.nature.com/articles/srep04547), Scientific Reports, vol 4:4547 (2014).
For computation of the graphlets (i.e., small induced subgraphs), the orca package is used, as introduced in
* [5] Hocevar & Demsar, [A combinatorial approach to graphlet counting](https://academic.oup.com/bioinformatics/article/30/4/559/205331), Bioinformatics, vol 30:4,559--565 (2014).
The github CRAN read-only mirror for the orca package can be found [here.](https://github.com/cran/orca)
* [6] Hocevar & 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)
The orca homepage with supporting information can be found [here.](http://www.biolab.si/supp/Rorca/)
Please cite these papers when using (variations of) this code for similar analysis pipelines.