scGEAToolbox - a Matlab toolbox for single-cell RNA-seq data analyses

📌 Installation Guide

There are four ways to install scGEAToolbox:

🔹 Method 1: Install as a MATLAB Add-On (Recommended)

1. Open the Add-On Explorer

   • In MATLAB, go to the Home tab.
   • Click on the Add-Ons icon to open the Add-On Explorer.

2. Search for scGEAToolbox

   • In the search bar, type "scGEAToolbox" and press Enter.

3. Select and Install

   • Find "scGEAToolbox (single-cell Gene Expression Analysis Toolbox)" in the results.
   • Click the Add button to install the toolbox.

4. Verify Installation

   • In MATLAB, type the following command in the Command Window to check installed toolboxes:

     ver

   • Look for scGEAToolbox in the list.

5. Launch scGEAToolbox

   • To start using scGEAToolbox, enter:

     scgeatool

   • This will open the graphical user interface for single-cell transcriptomic data analysis.

🔹 Method 2: Install via MATLAB Add-On (.mltbx)

1. Download scGEAToolbox.mltbx from:

   • 🔗 GitHub Releases
   • 🔗 MATLAB File Exchange

2. Install the toolbox:

   • Double-click scGEAToolbox.mltbx
   • MATLAB will open the Add-On Manager
   • Click Install

3. Verify the installation by running:

   matlab.addons.installedAddons

   Ensure scGEAToolbox appears in the list and added to the MATLAB path.

4. Verify the installation by running:

   scgeatool

🔹 Method 3: Install from Source (ZIP File)

1. Download the latest version from GitHub:

   • 🔗 GitHub Releases

2. Extract the ZIP file to your desired location, e.g.:

   C:\Users\yourusername\Documents\MATLAB\scGEAToolbox

3. Add the toolbox to the MATLAB path

   addpath('C:\Users\yourusername\Documents\MATLAB\scGEAToolbox')
   savepath

4. Verify the installation by running:

   scgeatool

🔹 Method 4: Install via GitHub (For Developers)

1. Run the following code in MATLAB:

   unzip('https://github.com/jamesjcai/scGEAToolbox/archive/main.zip');  

2. Add the toolbox to the MATLAB path

   addpath('./scGEAToolbox-main');
   savepath(fullfile(userpath,'pathdef.m'));
   % savepath;

Getting Started Quickly Using the SCGEATOOL App

Run the following code in MATLAB to start

scgeatool

Read Documentation

scGEAToolbox Documentation

SEE ALSO - Standalone Application

SCGEATOOL.exe is a standalone application running on Windows machines that do not have MATLAB installed. SCGEATOOL is a lightweight and blazing fast desktop application that provides interactive visualization functionality to analyze single-cell transcriptomic data. SCGEATOOL allows you to easily interrogate different views of your scRNA-seq data to quickly gain insights into the underlying biology. SCGEATOOL is a pre-compiled standalone application developed in MATLAB. Pre-compiled standalone releases are meant for those environments without access to MATLAB licenses. Standalone releases provide access to all of the functionality of the SCGEATOOL standard MATLAB release encapsulated in a single application. SCGEATOOL is open-sourced to allow you to experience the added flexibility and speed of the MATLAB environment when needed.

Help

If you have any questions or require assistance using scGEAToolbox, please contact me.

Citation

Cai JJ. scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. Bioinformatics. 2019;btz830. doi:10.1093/bioinformatics/btz830