Use the loupe cell browser to view the results of 10x single cell transcriptome analysis

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10X genomics The company not only provides a supporting platform for the analysis of single cell transcriptome data cell Ranger Software , At the same time, it also provides a special analysis result viewing software -Loupe Cell Browser, The software is a graphical interface software , The operation is very convenient , Support windows and mac Two operating systems , The download address is as follows

​ ​https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest​​

Once installed , Double click start up , The interface is as follows

stay cell ranger In the output of the software , There is one named ​​cloupe.cloupe​​ The file of , This file is used to input to Loupe Cell Browser In software .

Through the... In the upper left corner ​​File->Open File​​​, perhaps Browser for a Loupe Cell Browser File menu , Import the corresponding suffix ​​cloupe​​ The file of , The page after successful import is as follows

The default display is ​​t-SNE​​​ After the dimension reduction 2D-plot, The color of the cells depends on ​​Graph-Based​​​ Fill in the clustering results , For the result of clustering cluster, You can use the corresponding radio box , To adjust whether the... Is displayed in the figure cluster Corresponding cell , Colors can also be edited , Change colors , Through the triangle pull-down button , You can view the results of other clusters , such as ​​K-means​​ The result of clustering .

Detailed results of clustering , That is, each cell corresponds to cluster Number , You can export to a file through the rightmost button , The result is ​​CSV​​ Format , The contents are as follows

The middle table shows feature  table, each cluster List of genes with significant differences , It is shown as follows

The list of down regulated genes is displayed by default , It can be set through options , It is shown as follows

It also provides hetamap Display results for , It is shown as follows

These are the basic functions of the software , Compared with the display results of the web page , The software is more interactive , It is more convenient to explore data , Please refer to the official documentation for more functions and usage .

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