<h1 align="left">CyteType</h1>
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---
CyteType is a Python client for deep characterization of cell clusters from single‑cell RNA‑seq. It prepares your `AnnData` and calls an upstream hosted service to generate rich annotations, ontology terms, and an HTML report.
- Minimal install: `pip install cytetype`
## Quick Start
```python
import anndata
import scanpy as sc
from cytetype import CyteType
# ------ Example Scanpy Pipeline ------
# Skip this step if you already have clusters and marker genes in an AnnData object.
adata = anndata.read_h5ad("path/to/your/data.h5ad")
sc.pp.normalize_total(adata, target_sum=1e4)
sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata, n_top_genes=1000)
sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.leiden(adata, key_added="clusters")
sc.tl.rank_genes_groups(adata, groupby="clusters", method="t-test")
# ------ Example Scanpy Pipeline ------
# ------ CyteType ------
annotator = CyteType(adata, group_key="clusters")
adata = annotator.run(
study_context="Brief study description (e.g., Human brain tissue ...)",
)
# View results
print(adata.obs.cytetype_annotation_clusters)
print(adata.obs.cytetype_cellOntologyTerm_clusters)
```
## Documentation
- Configuration (LLMs, auth, advanced): <a href="docs/configuration.md">docs/configuration.md</a>
- Results: <a href="docs/results.md">docs/results.md</a>
- Examples & Colab Notebooks: <a href="docs/examples.md">docs/examples.md</a>
- Troubleshooting: <a href="docs/troubleshooting.md">docs/troubleshooting.md</a>
- Development: <a href="docs/development.md">docs/development.md</a>
- Server Overview (high‑level): <a href="docs/server-overview.md">docs/server-overview.md</a>
- Ollama Integration: <a href="docs/ollama.md">docs/ollama.md</a>
## Example Report
- Live sample: <a href="https://nygen-labs-prod--cytetype-api.modal.run/report/5b4eb3e1-fde7-4609-8be0-2bea015c241d?v=250722" target="_blank">CyteType Report</a>
## License
Licensed under CC BY‑NC‑SA 4.0 — see <a href="LICENSE.md">LICENSE.md</a>.
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"description": "<h1 align=\"left\">CyteType</h1>\n\n<p align=\"left\">\n <a href=\"https://github.com/NygenAnalytics/cytetype/actions/workflows/publish.yml\">\n <img src=\"https://github.com/NygenAnalytics/cytetype/actions/workflows/publish.yml/badge.svg\" alt=\"CI Status\">\n </a>\n <a href=\"https://github.com/NygenAnalytics/cytetype/blob/main/LICENSE\">\n <img src=\"https://img.shields.io/badge/License-CC%20BY--NC--SA%204.0-lightgrey.svg\" alt=\"License: CC BY-NC-SA 4.0\">\n </a>\n <a href=\"https://pypi.org/project/cytetype/\">\n <img src=\"https://img.shields.io/pypi/v/cytetype.svg\" alt=\"PyPI version\">\n </a>\n <img src=\"https://img.shields.io/badge/python-\u22653.11-blue.svg\" alt=\"Python Version\">\n</p>\n\n---\n\nCyteType is a Python client for deep characterization of cell clusters from single\u2011cell RNA\u2011seq. It prepares your `AnnData` and calls an upstream hosted service to generate rich annotations, ontology terms, and an HTML report.\n\n- Minimal install: `pip install cytetype`\n\n## Quick Start\n\n```python\nimport anndata\nimport scanpy as sc\nfrom cytetype import CyteType\n\n# ------ Example Scanpy Pipeline ------\n# Skip this step if you already have clusters and marker genes in an AnnData object. \nadata = anndata.read_h5ad(\"path/to/your/data.h5ad\")\nsc.pp.normalize_total(adata, target_sum=1e4)\nsc.pp.log1p(adata)\nsc.pp.highly_variable_genes(adata, n_top_genes=1000)\nsc.pp.pca(adata)\nsc.pp.neighbors(adata)\nsc.tl.leiden(adata, key_added=\"clusters\")\nsc.tl.rank_genes_groups(adata, groupby=\"clusters\", method=\"t-test\")\n# ------ Example Scanpy Pipeline ------\n\n# ------ CyteType ------\nannotator = CyteType(adata, group_key=\"clusters\")\nadata = annotator.run(\n study_context=\"Brief study description (e.g., Human brain tissue ...)\",\n)\n\n# View results\nprint(adata.obs.cytetype_annotation_clusters)\nprint(adata.obs.cytetype_cellOntologyTerm_clusters)\n```\n\n## Documentation\n- Configuration (LLMs, auth, advanced): <a href=\"docs/configuration.md\">docs/configuration.md</a>\n- Results: <a href=\"docs/results.md\">docs/results.md</a>\n- Examples & Colab Notebooks: <a href=\"docs/examples.md\">docs/examples.md</a>\n- Troubleshooting: <a href=\"docs/troubleshooting.md\">docs/troubleshooting.md</a>\n- Development: <a href=\"docs/development.md\">docs/development.md</a>\n- Server Overview (high\u2011level): <a href=\"docs/server-overview.md\">docs/server-overview.md</a>\n- Ollama Integration: <a href=\"docs/ollama.md\">docs/ollama.md</a>\n\n## Example Report\n- Live sample: <a href=\"https://nygen-labs-prod--cytetype-api.modal.run/report/5b4eb3e1-fde7-4609-8be0-2bea015c241d?v=250722\" target=\"_blank\">CyteType Report</a>\n\n## License\nLicensed under CC BY\u2011NC\u2011SA 4.0 \u2014 see <a href=\"LICENSE.md\">LICENSE.md</a>.\n",
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