Cell atlases such as Tabula Muris and Tabula Sapiens are multi-organ single cell omics data sets describing entire organisms. A cell atlas approximation is a lossy and lightweight compression of a cell atlas that can be streamed via the internet.
This project enables biologists, doctors, and data scientist to quickly find answers for questions such as:
- What types of cells populate the human heart?
- What is the expression of a specific gene across cell types in C elegans?
- What are the marker genes of a specific cell type in mouse pancreas?
- What fraction of cells (of a specific type) express a gene of interest?
To answer these questions, we construct approximations from all kinds of cell atlases using the code in this repo.
NOTE: At this stage, this repo is designed for internal use and made public for transparency. End users are expected to interact with the atlas approximations using the web interface or the API.
| Organism | Organs | Publication |
|---|---|---|
| homo sapiens | Bone marrow, heart, kidney, colon, pancreas, lung, tongue | https://www.science.org/doi/10.1126/science.abl4896 |
| mus musculus | Bone marrow, heart, kidney, colon, pancreas, lung, tongue | https://www.nature.com/articles/s41586-020-2496-1 |
| microcebus myoxinus | Bone marrow, heart, kidney, colon, pancreas, lung, tongue | https://www.biorxiv.org/content/10.1101/2021.12.12.469460v2 |
| caenorhabditis elegans | whole organism | https://www.science.org/doi/10.1126/science.aam8940 |
| drosophila melanogaster | Antenna, haltere, heart, intestines, leg, male reproductive glands, malpighian tubule, oenocyte, ovary, proboscis, skin, testis, trachea, wing | https://doi.org/10.1126/science.abk2432 |
| danio rerio | whole embryo | https://www.science.org/doi/10.1126/science.aar4362 |
| hofstenia miamia | whole organism | https://www.nature.com/articles/s41467-023-38016-4 |
| schmidtea mediterraea | whole organism | https://www.science.org/doi/10.1126/science.aaq1736 |
| schistosoma mansoni | whole organism | https://www.nature.com/articles/s41467-020-20794-w |
| spongilla lacustris | whole organism | https://www.science.org/doi/10.1126/science.abj2949 |
| stylophora pistillata | whole organism | https://www.sciencedirect.com/science/article/pii/S0092867421004402 |
| amphimedon queenslandica | whole organism | https://www.nature.com/articles/s41559-018-0575-6 |
| mnemiopsis leidy | whole organism | https://www.nature.com/articles/s41559-018-0575-6 |
| trichoplax adhaerens | whole organism | https://www.nature.com/articles/s41559-018-0575-6 |
| xenopus laevis | Bladder, bone marrow, brain, eye, heart, intestine, kidney, liver, lung, muscle, ovary, oviduct, pancreas, skin, spleen, stomach, testis | https://www.nature.com/articles/s41467-022-31949-2 |
If you would like to propose an additional cell atlas to be added to the list of approximations, please open an issue and specify:
- a hyperlink to a publication where the atlas is described
- a hyperlink to a data source where the table of counts can be downloaded
- any information you might have about cell type annotation
- the reason why you would like to have that atlas added here
Thank you for your time.