eudysbiome: Cartesian plot and contingency test on 16S Microbial data

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 <zhouxiaoyuan@picb.ac.cn>
License
GPL-2
Version
1.4.0

View on Bioconductor

Man pages

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...
eudysbiome
eudysbiome.
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

Files in this package

eudysbiome/DESCRIPTION
eudysbiome/NAMESPACE
eudysbiome/NEWS
eudysbiome/R
eudysbiome/R/Cartesian.R
eudysbiome/R/assignTax.R
eudysbiome/R/contingencyCount.R
eudysbiome/R/contingencyTest.R
eudysbiome/R/eudysbiome.R
eudysbiome/R/microAnnotate.R
eudysbiome/R/tableSpecies.R
eudysbiome/build
eudysbiome/build/vignette.rds
eudysbiome/data
eudysbiome/data/diffGenera.rda
eudysbiome/data/harmGenera.rda
eudysbiome/data/microCount.rda
eudysbiome/data/microDiff.rda
eudysbiome/inst
eudysbiome/inst/NEWS
eudysbiome/inst/Rep
eudysbiome/inst/Rep/Silva_119_rep_set97_taxonomy.txt.bz2
eudysbiome/inst/doc
eudysbiome/inst/doc/eudysbiome.R
eudysbiome/inst/doc/eudysbiome.Rnw
eudysbiome/inst/doc/eudysbiome.pdf
eudysbiome/man
eudysbiome/man/Cartesian.Rd
eudysbiome/man/assignTax.Rd
eudysbiome/man/contingencyCount.Rd
eudysbiome/man/contingencyTest.Rd
eudysbiome/man/diffGenera.Rd
eudysbiome/man/eudysbiome.Rd
eudysbiome/man/harmGenera.Rd
eudysbiome/man/microAnnotate.Rd
eudysbiome/man/microCount.Rd
eudysbiome/man/microDiff.Rd
eudysbiome/man/tableSpecies.Rd
eudysbiome/vignettes
eudysbiome/vignettes/eudysbiome.Rnw