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A general overview of the portal and how to navigate it |
The cellxgene Data Portal is SaaS data publishing platform that is optimized for finding, explorating, and reusing single cell data that adhere to a common, minimal schema that facilitates easy, intuitive exploration and integration.
When entering the Data Portal, you land on the Collections Page, which lists the Collections hosted on the Data Portal and metadata that define the tissue, assay, disease, organism, and cell count for each collection.
Note: We are adding search and filter capability to the the Data Portal. For now, the current best way to find datasets from a particular author or tissue is to
CTRL + Fto find matching text on the page.
Clicking on a Collection name sends you to that collection's page, which contains a description, key links, and the datasets of the Collection:
Each dataset is described by the same metadata available at the collection level. In addition, two buttons (far right) enable each dataset to be downloaded and explored:
Clicking the download button launches a dialog that enables a dataset to be downloaded in h5ad (AnnData v0.7) and rds (Seurat v3) formats. All datasets adhere to the cellxgene single cell annotated data schema. Datasets can either be downloaded via the browser by clicking the blue download button or via the command line by pasting the provided curl command.
Clicking the explore button launches the Cellxgene Explorer in a new tab:
To learn how to explore and analyze a dataset using the Cellxgene Explorer, please see the Explorer Tutorials section of this documentation.
The Data Portal evolved from the COVID-19 data portal, a collaboration with the Wellcome Sanger Institute and The Human Cell Atlas that was developed to host single cell datasets that were useful to analyze how SARS-CoV2 infects cells in the face of the 2020 global pandemic. Since then, the cellxgene team has reacted to the need for a more generalized system that increases access to single cell data.