This package enhances analysis and visualisation of microbial community data in an environmental context. The major points of focus include: alpha diversity which is measured using the pre-existing indices and compared among conditions, ordination and beta dispersion of taxa abundance, differential abundance of taxa under different conditions using Kruskal-Wallis test, kernel based approach and the famous DESeq2 implementation, effects of environmental variables to community structure and determining sub communities in taxa at different taxonomic levels using network-wide statistical measures. The package builds on phyloseq class as the back-borne and ggplot2 for visualisation among other packages.
Package details |
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Maintainer | |
License | What license is it under? |
Version | 0.1 |
URL | http://www.github.com/umerijaz/microbiomeSeq |
Package repository | View on GitHub |
Installation |
Install the latest version of this package by entering the following in R:
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