Downloading 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.