1 Install package

if (!require("BiocManager"))

2 Introduction

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).

**KEGG enrichment analysis**

Figure 1: KEGG enrichment analysis

3 Getting Started Quickly

Run the application:


4 Supported Analysis

Also, MicrobiomeProfiler provides several enrich functions for optional analysis.

  • KEGG enrichment analysis
  • COG enrichment analysis
  • Microbe-Disease enrichment analysis
  • Metabo-Pathway 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

5 Case Study

5.1 Data input

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.