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CellAnnotator

Tests Coverage Documentation Pre-commit.ci

A tool to annotate cell types based on marker genes using OpenAI models.

Key features

  • Automatically annotate cells including type, state and confidence fields.
  • Generate consistent annotations across samples of your study.
  • Optionally infuse prior knowledge by providing information about your biological system.
  • Retrieve reliable results thanks to OpenAI structured outputs
  • Use pre-integration cell type labels to either score your integration quality (e.g. scIB metrics) or to guide your integration effort (e.g. scPoli, scANVI)

Installation

You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

  1. Install the latest development version:
pip install git+https://github.com/quadbio/cell-annotator.git@main

Getting started

After installation, head over to OpenAI to generate your API key

Keep this key private and don't share it with anyone. CellAnnotator will try to read the key as an environmental variable - either expose it to the environment yourself, or store it as an .env file anywhere within the repository where you conduct your analysis and plan to run CellAnnotator. The package will then use dotenv to export the key from the env file as an environmental variable.

Credits

This tool was inspired by Hou et al., Nature Methods 2024 and https://github.com/VPetukhov/GPTCellAnnotator.

Contact

If you found a bug, please use the issue tracker.