10x Genomics
Single Cell Immune Profiling

Cell Ranger, printed on 11/05/2024

What's New in Loupe V(D)J Browser 4.0

Loupe V(D)J Browser 4.0 has been updated to support changes to Cell Ranger 5.0, including V(D)J aggr and the new clonotype grouping algorithm.

Compatibility with Cell Ranger and Previous Loupe Versions

Loupe V(D)J Browser 4.0 is a required upgrade for processing data generated by the Cell Ranger 5.0 pipeline. Due to extensive changes to the underlying infrastructure, .vloupe files generated by Cell Ranger 4.0 and earlier Cell Ranger versions cannot be read into Loupe V(D)J Browser 4.0 or Loupe Browser 5.0.

Comparison Mode

Loupe V(D)J Browser 4.0 now allows for comparison of samples in files generated by the V(D)J aggr pipeline. Data can be divided into samples based on the columns in the aggregation CSV provided to the aggr pipeline, such as donor, origin, library ID, and any custom columns. A sample group dropdown has been added to all comparison mode charts, allowing for quick navigation.

For .vloupe files with a large number of samples, a new selection option will appear to enable displaying a subset of samples in a single view.

The clonotype frequency view is no longer accessible via a button in the sample table, but can still be found in the chart type dropdown. Selectors have now been added to the clonotype frequency chart to allow for quick switching between samples.

Clonotype Table Filtering

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 a number of 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.
• Graph-based clusters generated by the new reclustering feature in Loupe Browser 5.0 can now be used to filter the clonotype table as part of the existing cluster filter.

Chain View Updates

It’s now easier than ever to gain insights from the chain view. Rows in the chain view now represent exact subclonotypes instead of individual cells, meaning cells with identical immune receptor nucleotide sequences are now collapsed into a single row in the table. A Download Barcode List option is available when hovering over an exact subclonotype to see the full list of barcodes included in the row. Additionally, a donor reference is now visible between the universal reference and consensus. The donor reference only spans the length of the V gene.

Additional Features

• Improved performance across the application on datasets with a high number of cells.
• Refreshed appearance for several features.

Removed Feature

• The IGV plugin view has been removed from Loupe V(D)J Browser 4.0.