10x Genomics
Single Cell Gene Expression

Cell Ranger, printed on 12/22/2024

What's New in Loupe Browser 5.0

Changelog of 5.0.x releases

Filter and Recluster

Loupe Browser 5.0 has been updated to allow users to filter and recluster single-cell gene expression datasets. With Loupe's new intuitive, high-performance filtering and reclustering workflow, users can filter out low-quality cell barcodes, narrow on cell types of interest for a more focused study, and explore and share the results of their reanalysis, all interactively, without writing a single line of code.

The reclustering workflow allows for inclusion or exclusion of barcodes by:

• Precomputed or custom cluster membership
• UMI count
• Distinct feature count
• Mitochondrial UMI Fraction
• CSV upload list

The reclustering algorithm generates a new Louvain-based clustering and a t-SNE plot over the filtered dataset. Datasets with less than 10,000 cells should be processed in under two minutes, and Loupe supports reclustering operations on datasets as large as 100,000 cells.

For more information and a guide to the workflow, visit the filtering and reclustering page.

Integrated Gene Expression + V(D)J Clonotype Analysis Updates

Loupe Browser 5.0 includes updates to the clonotype table, with new filtering options and improved performance with high cell count .vloupe files.

Support for Cell Ranger 5.0 VDJ Datasets

Loupe Browser 5.0 now only supports the loading of VDJ clonotypes created with Cell Ranger 5.0 and later. Previous versions of Loupe Browser may be used to look at VDJ data generated by Cell Ranger 4.0 and earlier.

New Clonotype Table Filtering Options

Identify potential invariant natural killer T (iNKT) cells and mucosal-associated invariant T (MAIT) cells with a new clonotype table filter. The iNKT/MAIT evidence filter can be used to view clonotypes that contain any cells with supporting evidence in any of the TRA genes, TRA junctions, TRB genes, or TRB junctions of being an iNKT or MAIT cell. This filter is only visible for T cell datasets.

There are other powerful filtering options added in this release:

• The clonotype table can now be filtered by sample for .vloupe files generated by aggr.
• Clonotypes in B cell datasets can be filtered by light or heavy chain isotype.

Improvements For All Applications

Concurrent Installation with Previous Releases

Loupe Browser 5.0 can be installed concurrently with a currently installed version of Loupe Browser 4.0 or lower. This is required to be able to support visualization of VDJ data created by Cell Ranger 4.0 or earlier.

Differential Expression

Differential expression is now more intuitively tied to the active category. If a differential expression calculation has not been run for the currently selected category, the differential expression table and heatmap will appear blank and prompt you to run the calcuation, instead of showing the most recently calculated differential expression.

Changelog for Loupe Browser 5.0.x

Loupe Browser 5.0.1 (February 3, 2021)

• Adds support for pyramid TIFFs, or TIFFs with multiple pages of the same image at different resolutions, in the Visium manual aligner.
• Updates differential expression and violin plots to reflect currently visible data.
• More clearly indicates when differential expression has not yet been calculated for an active category or set of clusters.
• Fixes bug where differential expression fails when viewing data points not in the currently visible projection.
• Fixes bug where reclustering calculation never completes on certain Windows machines.
• Fixes bug when switching between feature plot and other projections.
• Fixes crash when deleting an imported projection in a multiome ATAC + gene expression dataset.
• Adds error message when an imported projection name duplicates an existing projection name (such as "tsne").
• Changes default export name for differential expression table.
• Updates the certificate on the Windows installer.