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eudysbiome (version 1.2.0)

Cartesian plot and contingency test on 16S Microbial data

Description

eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.

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Version

Version

1.2.0

License

GPL-2

Maintainer

Xiaoyuan Zhou

Last Published

February 15th, 2017

Functions in eudysbiome (1.2.0)

eudysbiome

eudysbiome.
assignTax

Taxonomic Classification
microDiff

Differential annotated genera with abundance variations among pair-wise condition comparisons
contingencyCount

Contingency Table Construction
harmGenera

Manually curated genera annotation table A data frame containing 235 genera annotated as "harmful" and the harmful species included in these genera.
microAnnotate

Genus Annotation
microCount

Microbial count contingency table
tableSpecies

Construct a Genus-Species Data Frame
contingencyTest

Contingency test for count data
diffGenera

Differential microbes in Genus-Species table A data frame containing 10 differential genera and the species included, which was to be annotated as "harmful" or "harmless".