Downloading Datasets

How to download datasets

From the Datasets search page, click on the row containing a dataset you are interested in viewing to open the dataset page. At the top of the dataset summary, click on Download Dataset to select the file type and download.

There are two file types available for download:

1. AnnData: an AnnData (.h5ad) file that contains the count matrix, embeddings and gene and cell metadata.
2. CAP-JSON: a JSON file that contains metadata for each cell annotation labelset in the dataset. The metadata includes information such as the marker genes used as evidence to annotate the cells, rationale for the annotation and information about the annotation method, e.g. manual or algorithmic.

See the cell-annotation-schema GitHub repo for more information.

Disable downloading of datasets

If you do not wish for other users to be able to download your dataset, you can disable this function for draft workspaces and publications. Only users with Owner or Admin privileges can turn this feature on and off.

1. To disable dataset downloading, click on the More Actions button to the right of the datasets preview and select Disable Downloads.

2. To re-enable dataset download, click on the More Actions button and select Enable Downloads.