umerijaz/microbiomeSeq: Microbial community analysis in an environmental context.
Version 0.1

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.

Getting started

Package details

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umerijaz/microbiomeSeq documentation built on Jan. 22, 2018, 3:37 p.m.