10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC6.3, printed on 11/23/2024

Interoperability

There are many scripts and packages in the single cell analysis ecosystem. You may want to import and export projections, categorical labels, gene lists and filters into and out of Loupe Browser. Options to import and export data in Loupe Browser are usually inside a menu that is displayed after clicking a button with three vertical dots.

The types of data and formats that can be imported and exported from Loupe Browser are described here.

Projections

In Loupe Browser 3.1.0 and later, you can import custom projections. This allows you to compute a projection of the data using your favorite software packages like Seurat or Scanpy to compute UMAP, t-SNE, PCA, or MDS projections. You can also import layouts from trajectory inference methods.

The CSV format for importing projections is:

• Header is required
• First column: barcodes that are at least a subset of the barcodes in the .cloupe file
• Second column: numbers which represents the X coordinates
• Third column: numbers which represents the Y coordinates

Here is a simple example for a small subset of barcodes from the bundled AMLTutorial dataset.

Barcode,UMAP-1,UMAP-2
AAACATACGGTACT-1,-10.18537,-5.062836
AAACATTGCTCGCT-1,-7.0603027,2.789417
AAACATTGCTTCTA-1,-8.413968,-3.3959498
AAACATTGGCGATT-1,-3.0396965,-7.3784895
AAACCGTGCCTACC-1,-7.6169457,2.5746179

To import new projections, click on the action button to the right of the projection selector. Once a custom projection is uploaded, you are also able to rename it or delete it.

Categories

Loupe Browser allows you to import and export categories. This allows you to integrate clustering data from other pipelines or scripts, or export manually assigned categories into custom scripts. To do so, 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 format to create a categories CSV file is:

• First row must be a header
• A column header must be barcode and the column's contents must match at least a subset of the barcodes in the .cloupe file
• Addition column headers are category names and the column's contents are cluster labels.

barcode,id
AAACATACAGTACC-1,Monocytes
AAACCGTGTCGTGA-1,Monocytes
AAACATACCATTCT-1,Mature Ery
AAACATACTCGCAA-1,Mature Ery
AAACCGTGGCCATA-1,Mature Ery

In this case, the category name is "id" and the two clusters that are created are named "Monocytes" and "Mature Ery". You can also download a full example that you can import into the AMLTutorial dataset bundled with Loupe Browser. It is 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.

Feature lists

With Accessibility mode selected, you can choose to import a set of feature lists or export the currently loaded set of feature lists. Click on the Export button to the right of the feature list selector.

Filters

Filters can be imported and exported and used across datasets similarly to other features discussed on this page. However we recommend that you do not manually create filters. The filters use a JSON spec that is specific to Loupe Browser and is subject to modification.