# CyteBase

> Search a catalog of public single-cell datasets and open them as cloud-hosted CyteArc DataStores. This documentation is published from the master branch and covers the CyteBase SDK, its public releases, and the operator-only build pipeline.

Documentation revision: abe92a93ee6f586098196c484aad7221a7ce23e7. Links below open plain-text documentation.

- [Home](https://docs.nygen.io/CyteBase/index.txt): what the catalog contains and a first example

## Getting started

- [Installation](https://docs.nygen.io/CyteBase/installation/index.txt): Python requirements, plotting dependencies, releases and buckets, credentials, and network access
- [Explore CyteBase](https://docs.nygen.io/CyteBase/tutorials/cytebase/index.txt): search the catalog, open a published dataset remotely, read cell annotations, plot the imported UMAP and gene expression, and query the catalog with SQL
- [Analyze with CyteArc](https://docs.nygen.io/CyteBase/analyze-with-cytearc/index.txt): mount a small dataset as a writable CyteArc store with remote counts and run CyteArc's RNA pipeline on it

## Case studies

- [COVID-19 blood](https://docs.nygen.io/CyteBase/tutorials/cytebase-covid19/index.txt): compare COVID-19 and healthy donors using metadata, the published UMAP, and donor-level gene summaries

## API reference

- [API overview](https://docs.nygen.io/CyteBase/api/index.txt): exact public signatures and result contracts
- [CyteBase API](https://docs.nygen.io/CyteBase/api/cytebase.txt): releases, catalog queries, metadata-only DatasetEntry objects, remote DataStore access, writable mounts with remote counts, imported embedding helpers, and result tables

## Developers

- [Build pipeline](https://docs.nygen.io/CyteBase/developers/build-pipeline/index.txt): deploy and operate the Modal pipeline that ingests CELLxGENE datasets and builds CyteBase catalogs