Package: CoreMicrobiomeR 0.1.0
Mohammad Samir Farooqi
CoreMicrobiomeR: Identification of Core Microbiome
The Core Microbiome refers to the group of microorganisms that are consistently present in a particular environment, habitat, or host species. These microorganisms play a crucial role in the functioning and stability of that ecosystem. Identifying these microorganisms can contribute to the emerging field of personalized medicine. The 'CoreMicrobiomeR' is designed to facilitate the identification, statistical testing, and visualization of this group of microorganisms.This package offers three key functions to analyze and visualize microbial community data. This package has been developed based on the research papers published by Pereira et al.(2018) <doi:10.1186/s12864-018-4637-6> and Beule L, Karlovsky P. (2020) <doi:10.7717/peerj.9593>.
Authors:
CoreMicrobiomeR_0.1.0.tar.gz
CoreMicrobiomeR_0.1.0.tar.gz(r-4.5-noble)CoreMicrobiomeR_0.1.0.tar.gz(r-4.4-noble)
CoreMicrobiomeR_0.1.0.tgz(r-4.4-emscripten)CoreMicrobiomeR_0.1.0.tgz(r-4.3-emscripten)
CoreMicrobiomeR.pdf |CoreMicrobiomeR.html✨
CoreMicrobiomeR/json (API)
| # Install 'CoreMicrobiomeR' in R: |
| install.packages('CoreMicrobiomeR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 months agofrom:1df1ed8891. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 01 2024 |
| R-4.5-linux | OK | Sep 01 2024 |
Exports:CoreMicrobiomegroup_bar_plotssignificancestacked_bar_plotsvisualize
Dependencies:askpassbase64encbslibcachemcliclustercolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrDTedgeRevaluatefansifarverfastmapfastmatchfontawesomefsgenericsggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpermutepillarpkgconfigplotlyplyrpromisespurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownsassscalesshinyshinybusyshinycssloaderssourcetoolsSRSstatmodstringistringrsystibbletidyrtidyselecttinytexutf8vctrsveganviridisLitewithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identification of Core Microbiome | CoreMicrobiome |
| Arabidopsis thaliana - Metadata dataset | demo_md |
| Arabidopsis thaliana - OTU dataset | demo_otu |
| Arabidopsis thaliana - Taxonomy dataset | demo_tax |
| Grouped Bar Plots Based on Sample Size | group_bar_plots |
| Testing the Significance of the Identified Core Microbiome | significance |
| Stacked Bar Plots Based on Relative Abundance Data | stacked_bar_plots |
| Visualizing the effect of minimum count on the core size | visualize |