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.

AuthorXiaoyuan Zhou, Christine Nardini
Date of publicationNone
MaintainerXiaoyuan Zhou <zhouxiaoyuan@picb.ac.cn>
LicenseGPL-2
Version1.4.0

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Files

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

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