Package: metamicrobiomeR 1.1
metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across studies using random effect model
The metamicrobiomeR package implements Generalized Additive Model for Location, Scale and Shape (GAMLSS) with zero inflated beta (BEZI) family for analysis of microbiome relative abundance data (with various options for data transformation/normalization to address compositional effects) and random effect meta-analysis models for meta-analysis pooling estimates across microbiome studies. Random Forest model to predict microbiome age based on relative abundances of shared bacterial genera with the Bangladesh data (Subramanian et al 2014), comparison of multiple diversity indexes using linear/linear mixed effect models and some data display/visualization are also implemented.
Authors:
metamicrobiomeR_1.1.tar.gz
metamicrobiomeR_1.1.zip(r-4.5)metamicrobiomeR_1.1.zip(r-4.4)metamicrobiomeR_1.1.zip(r-4.3)
metamicrobiomeR_1.1.tgz(r-4.4-any)metamicrobiomeR_1.1.tgz(r-4.3-any)
metamicrobiomeR_1.1.tar.gz(r-4.5-noble)metamicrobiomeR_1.1.tar.gz(r-4.4-noble)
metamicrobiomeR_1.1.tgz(r-4.4-emscripten)metamicrobiomeR_1.1.tgz(r-4.3-emscripten)
metamicrobiomeR.pdf |metamicrobiomeR.html✨
metamicrobiomeR/json (API)
| # Install 'metamicrobiomeR' in R: |
| install.packages('metamicrobiomeR', repos = c('https://nhanhocu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nhanhocu/metamicrobiomer/issues
Last updated 4 years agofrom:17c800ac5b. Checks:OK: 1 ERROR: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 28 2024 |
| R-4.5-win | ERROR | Aug 28 2024 |
| R-4.5-linux | ERROR | Aug 28 2024 |
| R-4.4-win | ERROR | Aug 28 2024 |
| R-4.4-mac | ERROR | Aug 28 2024 |
| R-4.3-win | ERROR | Aug 28 2024 |
| R-4.3-mac | ERROR | Aug 28 2024 |
Exports:alpha.comparemeta.niceplotmeta.taxametatab.showmicrobiomeagepathway.compareread.multitaxa.comparetaxa.filtertaxa.mean.plottaxa.meansdntaxcomtab.show
Dependencies:askpassbase64encbayesmbitbit64bitopsbootbslibcachemcaretcaToolsclassclicliprclockcodetoolscolorspacecompositionsCompQuadFormcpp11crayoncurldata.tableDEoptimRdiagramdigestdplyre1071evaluatefansifarverfastmapfontawesomeforeachforeignfsfuturefuture.applygamlssgamlss.datagamlss.distgdatagenericsggplot2globalsgluegowergplotsgridExtragtablegtoolshardhathighrhmshtmltoolshttripredisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelavalifecyclelistenvlme4lmerTestlubridatemagrittrMASSmathjaxrMatrixmatrixStatsmemoisemetametadatmetaformgcvmimeminqaModelMetricsmunsellNADAnlmenloptrnnetnumDerivopensslparallellypbapplypillarpkgconfigplyrprettyunitspROCprodlimprogressprogressrproxypurrrR.cacheR.methodsS3R.ooR.utilsR6randomForestrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrrecipesrepmisreshape2rlangrmarkdownrobustbaserpartsas7bdatsassscalesshapeSQUAREMstringistringrsurvivalsystensorAtibbletidyrtidyselecttimechangetimeDatetinytextruncnormtzdbutf8vctrsviridisLitevroomwithrxfunxml2yamlzCompositions
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compare multiple alpha diversity indexes between groups | alpha.compare |
| Nice meta-analysis plots. | meta.niceplot |
| Meta-analysis of taxa/pathway abundance comparison. | meta.taxa |
| Display meta-analysis results. | metatab.show |
| Predict microbiome age. | microbiomeage |
| Compare (kegg) pathway abundance | pathway.compare |
| Read multiple files | read.multi |
| Compare taxa relative abundance | taxa.compare |
| Filter relative abundance data | taxa.filter |
| Plot mean taxa abundance | taxa.mean.plot |
| Summarize abundance by group | taxa.meansdn |
| Display abundance comparison results. | taxcomtab.show |
