OntoAnno#

Start here if you have a Seurat object and want to annotate cell types.

OntoAnno is a local web app for single-cell annotation. You give it a Seurat .rds file, a small YAML config, and an API key. OntoAnno then runs the annotation workflow, helps you review the labels, and creates a final HTML report.

Acknowledgement#

OntoAnno builds on the GPTAnno annotation workflow. For the original GPTAnno repository, see GPTAnno.

OntoAnno overview

What You Need#

Before starting, prepare these three things:

Item

What it means

A Seurat object

One .rds file saved from R, for example my_dataset.rds.

Dataset information

Species, tissue name, and where you want results to be saved.

LLM API key

Usually an OpenAI API key stored in OPENAI_API_KEY or in .env.

Workflow Guidelines#

For most users, follow these three steps in order:

  1. Install OntoAnno.

  2. Configure your dataset.

  3. Use the agent to run annotation and review labels.