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Introduction

MicrobiomeProfiler is an R-shiny package based on clusterProfiler, is user-friendly tool for functional enrichment analysis in microbiome data (T Wu, et al., 2021).

Installation

Installation via BiocManager:

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("MicrobiomeProfiler")

Or install MicrobiomeProfiler from github using devtools :

## Note that having installed clusterProfiler,config,DT,enrichplot,golem,magrittr,shiny,shinyWidgets,shinycustomloader,htmltools,ggplot2
if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("YuLab-SMU/MicrobiomeProfiler")

Quick Guides

library(MicrobiomeProfiler)
run_MicrobiomeProfiler()

Reference

  • T Wu#, E Hu#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo*, G Yu*. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141. doi: 10.1016/j.xinn.2021.100141