Introduction

In DSH’s plugin ecosystem, for biomedical data analysis scenarios, directly handling the metadata, statistical features, or raw data of AnnData objects in a conversation often requires structured tool support. The xby-anndata plugin uses the MCP protocol to provide agents with the ability to retrieve information about AnnData objects.

Plugin Positioning

The plugin is maintained by xby_skill and is released under the MIT license. It is an MCP-protocol-based data retrieval tool, primarily addressing the retrieval of AnnData object summaries, descriptive statistics, and viewing of raw data.

Core Features

The plugin provides the following four main tools:

  • set_xby_apikey
    Sets the API key in the chat. The key is persisted automatically and remains valid after restarting DSH.
  • view_raw_data
    Views the raw data of a specified AnnData object.
  • get_summary
    Retrieves summary information for an AnnData object from a file path or URL.
  • get_descriptive_stats
    Provides basic descriptive statistics for AnnData object attributes or attribute values (with optional filtering), including count, mean, standard deviation, minimum, maximum, and so on, or provides value counts.

Installation and Enablement

Installing from GitHub is recommended.

dsh plugin --profile web add github:xby_skill/xby-anndata

If you need local development and debugging, you can use one of the following methods:
1. Install from a local directory:

   dsh plugin --profile web add /absolute/path/to/xby-anndata
  1. Debug through cordis.patch.yml:
   dsh web --profile web --patch /absolute/path/to/dsh-ocr-plugin/cordis.patch.yml

Configuration and Usage

Before using this plugin, register on the Xiaobenyang official website to obtain an API key. When invoking the relevant tools in a conversation, the system will prompt you to set the key.

Notes

  • This plugin runs with the permissions of the current DSH process. Please check the source code and license (MIT) before use.
  • Local development and debugging methods are provided, making it suitable for secondary development or troubleshooting.

Conclusion

By following the steps above, you can achieve standardized retrieval and analysis of AnnData objects in a DSH environment. For more details, see the GitHub repository.