if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("MicrobiomeProfiler")
MicrobiomeProfiler is a functional enrichment tool for microbiome data based
clusterProfiler. It is an R/shiny package with user-friendly interface.
As showed in the following figure, the sidebar panel was the input options and the main panel was designed to show output results (Also can be seen in other analysis).
Run the application:
MicrobiomeProfiler provides several enrich functions for optional analysis.
There are four reference gene catalogs collected from publications that can be used as universe for KEGG analysis in specific scenarios.
|Reference Gene Catalog||Description|
|human_gut2014||Integrated non-redundant gene catalog of human gut microbiome published on Natrue Biotechnology in 2014|
|human_gut2016||Integrated non-redundant gene catalog of human gut microbiome published on Cell Systems in 2016|
|human_skin||Integrated human skin microbial non-redundant gene catalog|
|human_vagina||a comprehensive human vaginal non-redundant gene catalog (VIRGO) that includes 6751 KEGG orthology|
To click the
Example button, the example gene list would be showed in the input area. Also, more parameters can be set below the input area, for instance, p value cutoff. There is a customer_defined_universe choice for users to define the specific universe for enrichment analysis (Also for other enrichment analysis). After that, clicking the
Submit button to process analysis. The
Clean button was designed for cleaning the current results.