An R/shiny package for microbiome functional enrichment analysis

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Documentation for package ‘MicrobiomeProfiler’ version 1.19.2

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available_datasets List configured external datasets
clear_dataset_cache Remove cached external dataset artifacts
dataset_cache_info Summarize the local external data cache
download_dataset Download an external dataset into the local cache
enrichBugSigDB BugSigDB enrichment analysis for microbiome data
enrichCOG COG enrichment analysis for microbiome data
enrichEggNOG eggNOG-based KEGG pathway enrichment for microbiome data
enrichHMDB Metabolism enrichment analysis for microbiome data
enrichKO KO enrichment for microbiome data
enrichMBKEGG Metabolism enrichment analysis for microbiome data
enrichMDA Microbe-Disease associations enrichment analysis
enrichModule Module enrichment for microbiome data
enrichSMPDB Metabolism enrichment analysis for microbiome data
gseCOG COG GSEA enrichment analysis for microbiome data
gseEggNOG GSEA with eggNOG-based KEGG pathway annotations
gseHMDB Metabolism GSEA enrichment analysis for microbiome data
gseKO KO GSEA enrichment for microbiome data
gseMBKEGG Metabolism GSEA enrichment analysis for microbiome data
gseMDA Microbe-Disease associations GSEA enrichment analysis
gseModule Module GSEA enrichment for microbiome data
gseSMPDB Metabolism GSEA enrichment analysis for microbiome data
gson_cpd gson_cpd
gson_enzyme gson_enzyme
gson_KO gson_KO
gson_module gson_module
microbiota_data Example data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples
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
run_MicrobiomeProfiler Run the Shiny Application