eudysbiome: Cartesian plot and contingency test on 16S Microbial data
Version 1.6.0

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.

AuthorXiaoyuan Zhou, Christine Nardini
Date of publicationNone
MaintainerXiaoyuan Zhou <zhouxiaoyuan@picb.ac.cn>
LicenseGPL-2
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("eudysbiome")

Popular man pages

assignTax: Taxonomic Classification
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...
See all...

All man pages Function index File listing

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

Functions

Cartesian Man page Source code
assignTax Man page Source code
contingencyCount Man page Source code
contingencyTest Man page Source code
diffGenera Man page
eudysbiome Man page
eudysbiome-package Man page
harmGenera Man page
microAnnotate Man page Source code
microCount Man page
microDiff Man page
tableSpecies Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Cartesian.R
R/assignTax.R
R/contingencyCount.R
R/contingencyTest.R
R/eudysbiome.R
R/microAnnotate.R
R/tableSpecies.R
build
build/vignette.rds
data
data/diffGenera.rda
data/harmGenera.rda
data/microCount.rda
data/microDiff.rda
inst
inst/NEWS
inst/Rep
inst/Rep/Silva_119_rep_set97_taxonomy.txt.bz2
inst/doc
inst/doc/eudysbiome.R
inst/doc/eudysbiome.Rnw
inst/doc/eudysbiome.pdf
man
man/Cartesian.Rd
man/assignTax.Rd
man/contingencyCount.Rd
man/contingencyTest.Rd
man/diffGenera.Rd
man/eudysbiome.Rd
man/harmGenera.Rd
man/microAnnotate.Rd
man/microCount.Rd
man/microDiff.Rd
man/tableSpecies.Rd
vignettes
vignettes/eudysbiome.Rnw
eudysbiome documentation built on May 20, 2017, 10:07 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.