How to use Loupe Cell Browser to view the results of 10X single cell transcriptome analysis

How to use Loupe Cell Browser to view the results of 10X single-cell transcriptome analysis, I believe that many inexperienced people are at a loss about this. Therefore, this paper summarizes the causes and solutions of the problem. Through this article, I hope you can solve this problem.

Loupe Cell Browser, the software is a graphical interface software, the operation is very convenient, support windows and mac two operating systems.

After installation, double-click to start, and the interface is as follows

In the output of the cell ranger software, there is a file called cloupe.cloupe, which is used to input into the Loupe Cell Browser software.

Import the file with the corresponding suffix cloupe through the File- > Open File in the upper left corner, or the Browser for a Loupe Cell Browser File menu. The page after successful import is as follows

The default display is the 2D-plot after t-SNE dimensionality reduction, and the color of the cells is filled according to the results of Graph-Based clustering. For the clustering cluster, you can use the corresponding checkbox to adjust whether the corresponding cells of the cluster are displayed in the graph, and the color can also be edited to change different colors. Through the drop-down button of the triangle, you can view the results of other clusters, such as the results of K-means clustering.

The detailed result of clustering, that is, the corresponding cluster number of each cell, can be exported to a file through the rightmost button. The result is in CSV format, as shown below.

The middle table shows feature table, the list of genes that differ significantly under each cluster, as shown below

The list of down-regulated genes is displayed by default, which can be set by option, as shown below

At the same time, the display result of hetamap is provided, which is shown below.

These are the basic functions of the software. Compared with the display results of the web page, the software is more interactive and can explore data more conveniently.

After reading the above, have you mastered how to use Loupe Cell Browser to view the results of 10X single-cell transcriptome analysis? If you want to learn more skills or want to know more about it, you are welcome to follow the industry information channel, thank you for reading!