This repo contains some R scripts for analyzing metagenome datasets.

Table of Contens:

1. Centered Log-Ratio (CLR) Transformation[^1]
2. Ordination analysis
   • Visualise beta-diversity: NMDS, PCA, PCoA
   • Compute statistical significance of beta-diversity: ANOSIM, Adonis
   • Model the effect of environmental factors on microbiome: RDA

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Example file:

An example file folder can be found in here.

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Reference

[^1] Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. Microbiome Datasets Are Compositional: And This Is Not Optional. Front Microbiol 8, 2224 (2017).