ClusterProfShinyORA

clusterProfiler Over-representation analysis R shiny
This is part of the NASQAR toolbox
Pre-print: NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

This is a web-based interactive application that wraps the popular clusterProfiler package which implements methods to analyze and visualize functional profiles of genomic coordinates, gene and gene clusters.

Users can upload their own differential gene expression (DGE) data from DESeq2 or import data from the upstream Deseq2Shiny app.

This app allows for quick and easy Over-representation analysis (ORA) of GO-Terms and KEGG pathways.

It is meant to provide an intuitive interface for researchers to easily upload, analyze, visualize, and explore single-cell RNA-seq data interactively with no prior programming knowledge in R.

Visuals produced include dot plots, wordclouds, category net plots, enrichment map plots, GO induced graphs, gsea plots, and enriched KEGG pathway plots using the Pathview package.

The application follows this tutorial

See below for example output plots.

Input Data Types

This application accepts the following types of input data:

1. Example data (Demo):

For demo purposes, you can select "Example data"
You can follow the steps afterwards to run the analysis mirroring the tutorial in order to get familiar with the app

2. Upload your own data (gene counts):

A .csv/.txt file that contains a table of differential gene expression (DGE) data
Eg. the output of DESeq2
The file can be either comma or tab delimited
The required columns are Gene name/id, Log2 Fold Change, p-adjusted values
You will have to select the column names that match the above required columns
For a sample file, click here

Figure 2: Eg. DGE data file

Run Results

1. Data Output

The output results will be either displayed and/or is downloadable

EnrichGo results table
EnrichKEGG results table

2. Visualization

Various forms of visualizations are included for either Go/KEGG:

Bar Plot
Dot Plot
Enrichment Plot Map
Enriched GO induced graph (goplot, GO only)
Enriched GO induced graph (cnetplot)
Pathview Plots (KEGG)
Word Clouds

mfpfox / clusterprofshinyora Goto Github PK