DESCRIPTION

Package: microbiomeSeq
Title: Microbial community analysis in an environmental context.
Version: 0.1
Authors@R: c(
    person("Alfred", "Ssekagiri", email = "assekagiri@gmail.com", role = "aut"),
    person("Umer", " Zeeshan Ijaz", email = "Umer.Ijaz@glasgow.ac.uk", role = "cre"))
Description: 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.
Depends: R (>= 3.2.3)
Imports: igraph (>= 1.1.2),
		 DESeq2 (>= 1.16.1),
		 KMDA,
		 vegan (>= 2.4),
		 phyloseq (>= 1.14.0),
		 WGCNA (>= 1.60),
		 fso (>= 2.0),
		 randomForest (>= 4.6),
		 data.table (>= 1.10.4),
		 reshape2 (>= 1.4.2),
		 gtable (>= 0.2.0),
		 ggplot2 (>= 2.2.1),
		 gridExtra (>= 2.2.1)
Suggests: R.rsp
VignetteBuilder: R.rsp
URL: http://www.github.com/umerijaz/microbiomeSeq
License: What license is it under?
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0