Gene Expression Plotter

Visualize and compare gene expression from standard transcriptome (RNA-Seq) data, cluster samples and genes, and infer enrichment of gene function in gene-sets.

Documentation -- Use it here

★ Overview

Gene Expression Plotter is a single page application (SPA) designed to allow custom visualizations of gene expression from transcriptome (RNA-Seq) data.

Typical RNA-seq pipelines output relatively large transcript abundance tables, that require the use of a programming language to shape and visualize the data as a way to better understand results.

This application provides a graphical user interface to upload, process, and plot tabular data outputs from tools like Kallisto, Sailfish, Salmon, and many others.

The user can also generate a custom expression table using e.g. Microsoft Excel and provide further information about the transcripts in an information table, including gene function, differential gene expression, and ontological annotations.

This tool enables clustering of genes or biological samples by correlation resulting in a heatmap visualization. Principal component analysis (PCA) and enrichment analyses can be carried out.

</> Develop

This project is being developed with React. An installed Node version equal to or greater than 12 is required.

Quick Start

# clone this repository
git clone git@github.com:usadellab/GeneExpressionPlots.git

# change to the repository folder
cd GeneExpressionPlots

# install node modules
yarn install

# start the development server
yarn dev

Available Commands

yarn dev                # start development server
yarn build   		        # build for production
yarn lint    		        # lint code using ESLint
yarn test-components    # run component unit tests
yarn test-integration   # run integration tests

Example Data

Example files to test the application functionality can be found in the examples folder. Find more information about these files and how to use them in the Documentation.