Pathway Enrichment Analysis

This shiny app performs a pathway enrichment analysis using KEGG and Reactom databases utilizing the geneset provided by you. Currently it only supports human genes.

Usage

The application is hosted on Shiny.io

Instructions to use

Insert a gene set file (text file with gene names seperated by a newline or paste gene set in the text area. Then change the options for pathway analysis or final figure.

Installation

You can also deploy the application in your local machine using R Studio and/or R.

Prerequisites

Following R packages are required to run this application

install.packages("shiny")
install.packages("data.table")
install.packages("ggplot2")
install.packages("dplyr")
install.packages("DT")
install.packages("ggrepel")
install.packages("shinycssloaders")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MAGeCKFlute")
BiocManager::install("ReactomePA")
BiocManager::install("clusterProfiler")
BiocManager::install("clusterProfiler")
BiocManager::install("org.Hs.eg.db")

Clone the repo and run the application.