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.
|Author||Xiaoyuan Zhou, Christine Nardini|
|Date of publication||None|
|Maintainer||Xiaoyuan Zhou <email@example.com>|
assignTax: Taxonomic Classification
Cartesian: 2-D Cartesian plane Plots
contingencyCount: Contingency Table Construction
contingencyTest: Contingency test for count data
diffGenera: Differential microbes in Genus-Species table A data frame...
harmGenera: Manually curated genera annotation table A data frame...
microAnnotate: Genus Annotation
microCount: Microbial count contingency table
microDiff: Differential annotated genera with abundance variations among...
tableSpecies: Construct a Genus-Species Data Frame