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10x Genomics
Chromium Single Cell Multiome ATAC + Gene Exp.

What is Loupe Browser?

Introduction

Loupe Browser is a desktop application for Windows and MacOS that allows you to quickly and easily visualize and analyze 10x Chromium™ Single Cell Multiome ATAC + GEX data. It combines the tools previously developed for looking at Single Cell Gene Expression and Single Cell ATAC data, and adds functionality to allow users to easily connect and relate gene expression and ATAC data generated for the same cells.

Loupe is named for a jeweler's loupe, which is used to inspect gems.

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

To walk through the features and uses of Loupe Browser for Single Cell Multiome ATAC + Gene Expression data, start the multiome tutorial.

Loupe Browser can also be used to analyze Chromium™ Single Cell 5′ and 3′ gene expression, immune profiling data, and Visium data. To learn how, you can visit the Loupe documentation pages for:

Finally, if you have already used Loupe Browser to investigate gene expression or ATAC, and are looking at multiomic data for the first time, read Multiome Data Concepts.