API for cell atlas approximations

Cell atlases are single cell omics data sets describing multiple organs and ideally entire organisms. A cell atlas approximation is a lightweight, lossy compression of a cell atlas that retains key informtation while reducing data size and complexity.

Note

While approximations are currently limited to single cell transcriptomic data, future support for chromatin accessibility and other single-cell assays is planned, with much of the code infrastructure already set up.

Because of their small size, atlas approximations are well suited for acess over a RESTful API, which is described in this page.

Note

To access cell atlas approximations using a Human Interface (HI) instead, check out our friendly chat bot @ https://atlasapprox.org. Please be nice to the bot 😊 - it’s not very smart yet.

Examples of API usage:

  • Ask the average expression of a set of genes in a cell type, organ, and organism.

  • List the cell types across an entire organism that have the highest expression of a certain gene.

  • Find marker genes for a specific cell type.

  • Show a table of which cell types are found in multiple tissues (e.g. various kinds immune cells).

Version

The most recent version of the API is v1.

Interfaces

There are multiple ways to access atlas approximations programmatically:

Note

All interfaces use the REST API internally and provide a convenience layer for users of specific languages.

Embedding in a web page

It is relatively easy to embed API calls to cell atlas approximations in a web page through the JavaScript and REST interfaces:

Authors

Fabio Zanini @ fabilab.

Citation

Ying Xu and Fabio Zanini. Lightweight and scalable approximations democratise access to single cell atlases. In preparation (2023).

Data Sources