Package: MicrobiomeProfiler 1.11.0
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:
MicrobiomeProfiler_1.11.0.tar.gz
MicrobiomeProfiler_1.11.0.zip(r-4.5)MicrobiomeProfiler_1.11.0.zip(r-4.4)MicrobiomeProfiler_1.11.0.zip(r-4.3)
MicrobiomeProfiler_1.11.0.tgz(r-4.4-any)MicrobiomeProfiler_1.11.0.tgz(r-4.3-any)
MicrobiomeProfiler_1.11.0.tar.gz(r-4.5-noble)MicrobiomeProfiler_1.11.0.tar.gz(r-4.4-noble)
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MicrobiomeProfiler.pdf |MicrobiomeProfiler.html✨
MicrobiomeProfiler/json (API)
# Install 'MicrobiomeProfiler' in R: |
install.packages('MicrobiomeProfiler', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yulab-smu/microbiomeprofiler/issues
- 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
- microbiota_taxlist - Example data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples
On BioConductor:MicrobiomeProfiler-1.11.0(bioc 3.20)MicrobiomeProfiler-1.10.0(bioc 3.19)
Last updated 2 months agofrom:0b41aed7ff
Exports:enrichCOGenrichHMDBenrichKOenrichMBKEGGenrichMDAenrichModuleenrichSMPDBrun_MicrobiomeProfiler
Dependencies:AnnotationDbianytimeapeaplotaskpassattemptbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemcliclusterProfilercodetoolscolorspacecommonmarkconfigcowplotcpp11crayoncrosstalkcurldata.tableDBIdigestDOSEdownloaderdplyrDTenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglueGO.dbgolemGOSemSimgraphlayoutsgridExtragridGraphicsgsongtableHDO.dbherehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrpngpolyclippromisespurrrqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrmarkdownrprojrootRSQLiteS4VectorssassscalesscatterpieshadowtextshinyshinycustomloadershinyWidgetssnowsourcetoolsstringistringrsyssystemfontstibbletidygraphtidyrtidyselecttidytreetinytextreeiotweenrUCSC.utilsutf8vctrsviridisviridisLitewithrxfunxtableXVectoryamlyulab.utilszlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Functional enrichment analysis for microbiome data | MicrobiomeProfiler-package MicrobiomeProfiler |
COG enrichment analysis for microbiome data | enrichCOG |
Metabolism enrichment analysis for microbiome data | enrichHMDB |
KO enrichment for microbiome data | enrichKO |
Metabolism enrichment analysis for microbiome data | enrichMBKEGG |
Microbe-Disease associations enrichment analysis | enrichMDA |
Module enrichment for microbiome data | enrichModule |
Metabolism enrichment analysis for microbiome data | enrichSMPDB |
gson_cpd | gson_cpd |
gson_enzyme | gson_enzyme |
gson_KO | gson_KO |
gson_module | gson_module |
Example data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples | microbiota_data microbiota_taxlist |
Example data: a vector of 134 significantly different functional COGs between Psoriasis patients and controls | Psoriasis_data |
Example data: a vector of 91 KEGG Orthologies (KOs) showing significant associations with weaning weight | Rat_data |
Run the Shiny Application | run_MicrobiomeProfiler |