Package: eudysbiome 1.37.0
Xiaoyuan Zhou
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.
Authors:
eudysbiome_1.37.0.tar.gz
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eudysbiome_1.37.0.tgz(r-4.4-any)eudysbiome_1.37.0.tgz(r-4.3-any)
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eudysbiome.pdf |eudysbiome.html✨
eudysbiome/json (API)
NEWS
| # Install 'eudysbiome' in R: |
| install.packages('eudysbiome', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- 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"'.
- harmGenera - Manually curated genera annotation table A data frame containing 260 genera annotated as "harmful" and the harmful species included in these genera.
- microCount - Microbial count contingency table
- microDiff - Differential annotated genera with abundance variations among pair-wise condition comparisons
On BioConductor:eudysbiome-1.37.0(bioc 3.21)eudysbiome-1.36.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:89cab1f436. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 04 2024 |
| R-4.5-win | NOTE | Dec 04 2024 |
| R-4.5-linux | NOTE | Dec 04 2024 |
| R-4.4-win | NOTE | Dec 04 2024 |
| R-4.4-mac | NOTE | Dec 04 2024 |
| R-4.3-win | NOTE | Dec 04 2024 |
| R-4.3-mac | NOTE | Dec 04 2024 |
Exports:assignTaxCartesiancontingencyCountcontingencyTestmicroAnnotatetableSpecies
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rmimeopensslplyrR.methodsS3R.ooR.utilsR6RcppRhtslibRsamtoolsS4VectorssnowsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Taxonomic Classification | assignTax |
| 2-D Cartesian plane Plots | Cartesian |
| Contingency Table Construction | contingencyCount |
| Contingency test for count data | contingencyTest |
| 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"'. | diffGenera |
| eudysbiome. | eudysbiome-package eudysbiome |
| Manually curated genera annotation table A data frame containing 260 genera annotated as "harmful" and the harmful species included in these genera. | harmGenera |
| Genus Annotation | microAnnotate |
| Microbial count contingency table | microCount |
| Differential annotated genera with abundance variations among pair-wise condition comparisons | microDiff |
| Construct a Genus-Species Data Frame | tableSpecies |