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CZ CELLxGENE / Human Cell Atlas
CELLxGENE and the Human Cell Atlas hold single-cell data from healthy and diseased tissue, browsable and downloadable.
Also called: CELLxGENECZ CELLxGENEHuman Cell AtlasHCACELLxGENE Census
Overview
CZ CELLxGENE and the Human Cell Atlas hold tens of millions of annotated single cells from healthy and diseased tissue, including tumour microenvironment datasets, all browsable and downloadable. The platform is run by the Chan Zuckerberg Initiative together with the HCA, and the data are released under CC BY. It is the basis for cell-type-level target expression work and immune atlas studies. On OnCo it is linked to the technology Single-cell and spatial profiling, the institutions Chan Zuckerberg Biohub, Max Delbrück Center for Molecular Medicine and Wellcome Sanger Institute, the Virtual cell roadmap and the bottleneck Cold tumours and the immunosuppressive microenvironment, as well as the idea An open foundation model of the cancer cell trained on perturbation data.
Holds
Tens of millions of single cells with annotations, including tumour microenvironment datasets.
Licence
CC BY
Maintainer
Chan Zuckerberg Initiative / HCA
Dataset registry
Size: Tens of millions of annotated single cells
Access: open
Consent and reuse: CC BY; donor consent handled by contributing studies.
All datasets and the models trained on them →Similar pages
- TechnologyNicheformer (spatial single-cell)
Shares Single-cell and transcriptome foundation models: UCE, GeneCompass, BulkFormer, BulkRNABert, Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell, Single-cell & spatial profiling.
- TermVirtual cell models and in-silico perturbation screens
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), An open foundation model of the cancer cell trained on perturbation data, Cancer AI vocabulary (CanSim terms map).
- TermArray and table formats: HDF5, Zarr, OME-Zarr, Parquet
Shares AnnData and h5ad files, Cancer AI vocabulary (CanSim terms map).
- TermFoundation model
Shares Single-cell and transcriptome foundation models: UCE, GeneCompass, BulkFormer, BulkRNABert, Single-cell RNA sequencing (scRNA-seq, 10x Chromium), Cancer AI vocabulary (CanSim terms map).
- TermSpatial transcriptomics platforms (Visium HD, Xenium, MERFISH, CosMx, CODEX)
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), Single-cell & spatial profiling, Cancer AI vocabulary (CanSim terms map).
- TermMondo disease ontology
Shares Uberon anatomy ontology and the Cell Ontology, Cancer AI vocabulary (CanSim terms map).
- TermHuman Phenotype Ontology (HPO)
Shares Uberon anatomy ontology and the Cell Ontology, Cancer AI vocabulary (CanSim terms map).
- Company10x Genomics
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), Single-cell & spatial profiling, Cold tumours and the immunosuppressive microenvironment.
technologies
institutions
terms
roadmaps
ideas
bottlenecks
Open-source projects
All open source in oncology →Open-source projects that are the code behind this collection or publish it, from OnCo's own catalogue: licence and last activity as the repository reported them on the day of the fetch. Listing is not endorsement; check the licence before reuse and the validation before clinical use.
The Chan Zuckerberg Initiative's interactive explorer for single-cell datasets, behind the CELLxGENE Discover portal.