Cell Ranger3.1, printed on 11/28/2022
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|
|Barcoding & Library
|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.
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.
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.