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10x Genomics
Chromium Single Cell ATAC

What is Loupe Cell Browser?


Loupe Cell Browser is a desktop application for Windows and MacOS that allows you to quickly and easily visualize and analyze 10x Chromium™ Single Cell ATAC data. It is optimized for finding significant peaks and distinguishing transcription factor motifs, identifying cell types, comparing chromatin accessibility between groups of cells, and exploring substructure within cell clusters. Loupe is named for a jeweler's loupe, which is used to inspect gems.

Loupe Cell Browser opens .cloupe files generated by the Cell Ranger ATAC pipeline. Once your data is in Loupe Cell Browser, you can rapidly explore and gain insights from the data without writing a line of code.

Loupe Cell Browser is built to accelerate the following applications:

To walk through the features and uses of Loupe Cell Browser for single-cell ATAC data, start the ATAC tutorial.

Loupe Cell Browser can also be used to analyze Chromium™ Single Cell 5′ and 3′ gene expression and immune profiling data. To learn how, consult the Loupe Cell Browser for Gene Expression page.

Finally, if you have already used Loupe Cell Browser to investigate gene expression, and are new to ATAC, you should read Differences from Gene Expression.