10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC3.1, printed on 11/14/2024

Interoperability

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

On this page, we enumerate the types of data that you can import and export into and out of Loupe Cell Browser and document the formats.

Projections

In Loupe Cell 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 as follows:

• 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

In Loupe Cell Browser 1.0.5 and later, you can both 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.

To create a categories CSV file the format is as follows:

• 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 the above case, the category name is named "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 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.

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 action button to the right of the feature list selector to do so:

Filters

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