> For the complete documentation index, see [llms.txt](https://docs.genomenexus.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.genomenexus.org/api.md).

# API ⚙️

A full listing of all API endpoints can be found here:

<https://www.genomenexus.org/swagger-ui.html>.

## API Clients

For access through Python/R see the notebooks here:

<https://github.com/genome-nexus/genome-nexus/tree/master/notebooks>

## Command Line Clients

There are two Command Line Clients available. One written in NodeJS which provides a simple user-friendly interface:

<https://github.com/genome-nexus/genome-nexus-cli>

There is also a Java Command Line Client which has been developed with a focus on internal processes at Memorial Sloan Kettering Cancer Center but might work for your use case as well:

<https://github.com/genome-nexus/genome-nexus-annotation-pipeline>

They are similar in terms of feature completeness

## Other Languages

The API follows the Swagger/Open API specification, so clients can be generated in most languages: <https://openapi-generator.tech/docs/generators>

## Applications build on top of the API

See the [tools section](/tools.md)