10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger3.1, printed on 12/22/2024

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 5′ and 3′ gene expression data. It is optimized for finding significant genes, identifying cell types, and exploring substructure within cell clusters. Loupe is named for a jeweler's loupe, which is used to inspect gems.

	10x Chromium	Sequencer	10x Cell Ranger	10x Loupe Cell Browser
Cell Suspension	Barcoding & Library Construction	Sequence library	Pipelines	Analysis & Visualization

Loupe Cell Browser opens .cloupe files generated by the Cell Ranger 1.3 (or later) pipelines, or by cellranger mkloupe for older pipelines. You may also import a sample's corresponding V(D)J clonotype data from Cell Ranger 2.1 or later. 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:

• Finding Significant Genes
  Determine genes that uniquely characterize clusters at the press of a button.
  

• Identifying Cell Types
  Use gene lists and the gene expression view to locate different cell types and functional groups.
  

• Exploring Substructure
  Create custom clusters and use differential expression tools to identify even smaller subgroups in your data.
  

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

• Integrated Gene Expression and V(D)J Analysis
  Combine gene expression and immune repertoire data from the same sample to gain new insights about complex disease.

• Sharing Results
  Save genes of interest, export data tables, and capture screenshots of your single-cell data.
  

To walk through the features and uses of Loupe Cell Browser, start the tutorial.