10x Genomics
Single Cell Gene Expression

Cell Ranger, printed on 04/25/2024

What's New in Loupe Cell Browser 1.0.5

Category Import and Export

We recognize that there are many scripts and packages in the single-cell analysis ecosystem, and that you may want to import and export labels into and out of Loupe Cell Browser. We've made this easy to do in Loupe Cell Browser 1.0.5. When Categories mode is active, simply click on the action button to the right of the active category name, and select from one of the import/export options:

The requirements on the CSV file are that barcodes must be in the first column, the first row must be a header, the barcode column header must be named barcode, and that the values of the barcodes must match at least a subset of the barcodes in the .cloupe file.

Here's an example that you can import into the AMLTutorial dataset bundled with Loupe Cell Browser. It's a set of manual annotations for the Patient sample. You can import multiple categories at once from a single CSV file; each column will encode its own category.

Renaming and Recoloring Clusters

You can now rename and recolor the clusters you create, or clusters automatically generated by the Cell Ranger pipeline. In Categories mode, right-click (Windows)or Ctrl-click (Mac) a label or color. A context menu will appear, and you'll be able to edit the cluster name or cluster color, as shown below:

Changes to Cell Ranger-derived clusters will appear as separate clusterings to users of older versions of Loupe Cell Browser.

Additional Fixes

• Loupe Cell Browser will now correctly open files with '+' in the name.
• Outbound links to Ensembl gene information should look correctly formatted (Thanks, Ensembl team!)
• More consistent color palettes for precomputed and user-created categories.