SCGEATOOL

SCGEATOOL is a lightweight and blazing fast MATLAB 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.

Overview

In MATLAB, scgeatool function can be used to start SCGEATOOL to visualize SCE class/object. Below are links to several case studies and examples using the scgeatool function to explore scRNA-seq data. All examples are below are publically available through GitHub.

Using SCGEATOOL to explore

For a quick exploratry data analysis using scgeatool function

cdgea;
load example_data\testXgs.mat
scgeatool(X,g,s)

where X is the expression matrix, g is the list of genes, and s is the coordinates of embedding.

You can also load an example SCE (SingleCellExperiment object) variable using the following code:

cdgea;
load example_data\testSce.mat
scgeatool(sce)

If everything goes right, you will see the main inferface of SCGEATOOL like this:

Making scRNA-seq data into SCE

SingleCellExperiment defines a Single-cell Experiment (SCE) class in order to store scRNAseq data and variables. To make an SCE class, you need two variables: \(X\) and \(g\), which are gene expression matrix and gene list, respectively.

cdgea;
load example_data\testXgs.mat
sce=SingleCellExperiment(X,g,s);
scgeatool(sce)

SCGEATOOL standalone for Windows

SCGEATOOL standalone 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.