- CellxGene
- Find Published Data
- Contribute and Publish Data
- Download Published Data
- Analyze Public Data
- Get Started
- Hosted Tutorials
- Gene Expression Documentation
- Annotate and Analyze Your Data
- Join the CellxGene User Community
- Cite cellxgene in your publications
- Frequently Asked Questions
- Learn About Single Cell Data Analysis
Downloading Published Data on CZ CELLxGENE Discover
Clicking the download button launches a dialog that enables a dataset to be downloaded in h5ad (AnnData v0.10) and rds (Seurat v5) formats. All datasets adhere to the CELLxGENE single cell annotated data schema.
Click the white Download button for the dataset that you wish to download.
Select either the h5ad (AnnData v0.10) or rds (Seurat v5) download format. Click the blue Download button to download the dataset via the browser. The permanent download link can also be copied, shared, and pasted into a browser address bar.
Deprecation of Seurat Downloads on CELLxGENE Discover
We are deprecating Seurat downloads on the CELLxGENE Discover platform, effective late 2024. While Seurat support has served many of our users, ongoing support has become unsustainable due to limitations in conversion tools and cross-ecosystem interoperability.This decision aligns with our shift towards a Python-based ecosystem, consistent with our Virtual Cell Platform (VCP) and Census strategies. As our platform increasingly supports new types of spatial and multimodal assays, focusing on Python will enable us to deliver a more consistent and scalable user experience.
Availability of Earlier Seurat Downloads
Please note that earlier Seurat downloads will continue to be available. Previous versions of datasets will not be removed, and any Seurat RDS files that were previously downloaded will remain accessible. These can still be accessed via their URL (encoded as a citation in the dataset's @misc slot) or through the Discover API (GET dataset versions). This ensures that any ongoing research is not disrupted.
Seurat Support
If you need to convert h5ad files to Seurat, there are some community-supported tools that can assist with this task, though we caution that these tools may be less stable. Please reach out to the Seurat community for supported methods of conversion from AnnData to Seurat formats. We appreciate your understanding as we continue to refine our platform for reliability and future growth.