10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC3.1, printed on 12/03/2024

What is Loupe Cell Browser?

Introduction

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:

• Identifying Cell Types
  Find promoters and transcription factor motifs that differentiate distinct cell types and functional groups using Accessibility mode.
   

• Exploring Cell Subtypes
  Use the filter panel to create complex boolean filters to find cell subtypes in your dataset.
   

• Analyzing Differential Accessibility
  Use the ATAC Peak Viewer to pinpoint the location of differentially accessible genomic regions with putative regulatory function.
   
• Finding Significant Features
  Create custom clusters and use differential accessibility tools to identify precise cell groups within your data.
   
• Sharing Results
  Save features of interest, export data tables, and capture screenshots of your single-cell ATAC data.
  

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.