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.
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[1] Mahana et al. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet, Genome Medicine, vol 8:48 (2016)
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[2] Ruiz et al., A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity, Nature Communications, vol 8:518 (2017)
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[3] Tipton, Müller, et al. Fungi stabilize connectivity in the lung and skin microbial ecosystems, 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.
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, Scientific Reports, vol 4:4547 (2014).
For computation of the graphlets (i.e., small induced subgraphs), the orca package is used, as introduced in
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[5] Hocevar & Demsar, A combinatorial approach to graphlet counting, Bioinformatics, vol 30:4,559--565 (2014). The github CRAN read-only mirror for the orca package can be found here.
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[6] Hocevar & Demsar, Computation of graphlet orbits for nodes and edges in sparse graphs, Journal of Statistical Software, vol 71:10 (2016) The orca homepage with supporting information can be found here.
Please cite these papers when using (variations of) this code for similar analysis pipelines.