Package: MicrobiomeProfiler 1.18.1

Guangchuang Yu

MicrobiomeProfiler: An R/shiny package for microbiome functional enrichment analysis

This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

Authors:Guangchuang Yu [cre, aut], Meijun Chen [aut]

MicrobiomeProfiler_1.18.1.tar.gz
MicrobiomeProfiler_1.18.1.zip(r-4.7)MicrobiomeProfiler_1.18.1.zip(r-4.6)MicrobiomeProfiler_1.18.1.zip(r-4.5)
MicrobiomeProfiler_1.18.1.tgz(r-4.6-any)MicrobiomeProfiler_1.18.1.tgz(r-4.5-any)
MicrobiomeProfiler_1.18.1.tar.gz(r-4.7-any)MicrobiomeProfiler_1.18.1.tar.gz(r-4.6-any)
MicrobiomeProfiler_1.18.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MicrobiomeProfiler/json (API)

# Install 'MicrobiomeProfiler' in R:
install.packages('MicrobiomeProfiler', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yulab-smu/microbiomeprofiler/issues

Datasets:
  • microbiota_taxlist - Example data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples
  • Psoriasis_data - Example data: a vector of 134 significantly different functional COGs between Psoriasis patients and controls
  • Rat_data - Example data: a vector of 91 KEGG Orthologies (KOs) showing significant associations with weaning weight

On BioConductor:MicrobiomeProfiler-1.19.1(bioc 3.24)MicrobiomeProfiler-1.18.1(bioc 3.23)

microbiomesoftwarevisualizationkegg

7.34 score 42 stars 42 scripts 15 exports 136 dependencies

Last updated from:ebd282865e (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR206
linux-devel-x86_64OK320
source / vignettesOK252
linux-release-x86_64OK302
macos-release-arm64OK139
macos-oldrel-arm64OK134
windows-develOK200
windows-releaseOK191
windows-oldrelOK210
wasm-releaseOK163

Exports:enrichCOGenrichHMDBenrichKOenrichMBKEGGenrichMDAenrichModuleenrichSMPDBgseCOGgseHMDBgseKOgseMBKEGGgseMDAgseModulegseSMPDBrun_MicrobiomeProfiler

Dependencies:aisdkAnnotationDbiapeaplotaskpassattemptbase64encBiobaseBiocGenericsBiostringsbitbit64blobbslibcachemcallrcliclusterclusterProfilercommonmarkconfigcpp11crayoncrosstalkcurlDBIdigestDOSEdplyrDTenrichitenrichplotevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbgolemGOSemSimgridGraphicsgsongtableherehighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemimenlmeopensslotelpatchworkpillarpkgconfigplyrpngpolyclipprocessxpromisespspurrrqvalueR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownrprojrootRSQLiteS4VectorsS7sassscalesscatterpieSeqinfoshinyshinycustomloadershinyWidgetssourcetoolsstringistringrsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextreeiotweenrutf8vctrsviridisLitewithrxfunxtableXVectoryamlyulab.utils

Introduction to MicrobiomeProfiler

Meijun Chen and GuangChuang Yu

Rendered fromMicrobiomeProfiler.Rmdusingknitr::rmarkdownon Jun 20 2026.

Last update: 2023-04-18
Started: 2021-09-17