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the Docs](https://img.shields.io/readthedocs/cellink/latest.svg?label=Read%20the%20Docs)](https://cellink-docs.readthedocs.io/)\n[![Test](https://github.com/theislab/cellink/actions/workflows/test.yaml/badge.svg)](https://github.com/theislab/cellink/actions/workflows/test.yaml)\n[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit\u0026logoColor=white)](https://github.com/pre-commit/pre-commit)\n\n# Single-cell Genetics Package (Cellink)\n\n\u003c!-- TODO comment back in once package is public --\u003e\n\u003c!-- [![Tests][badge-tests]][tests]\n\n\u003c!-- [badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/Single-cell Genetics (Cellink)/test.yaml?branch=main --\u003e\n\u003c!-- [![Documentation][badge-docs]][documentation]  --\u003e\n\u003c!-- [badge-docs]: https://cellink-docs.readthedocs.io/  --\u003e\n\nWelcome to the official documentation for **cellink**—the toolkit designed to bridge the gap between single-cell data and individual-level genetic analysis.\n\n## Motivation\n\nIntegrating genetic data with cellular heterogeneity is crucial for advancing personalized medicine. **cellink** provides the missing framework for efficiently handling and analyzing genetic variation alongside complex single-cell omics data at scale.\n\n## ✨ Key Features \u0026 Structure\n\n**cellink** introduces the `DonorData` class, unifying individual-level and single-cell data. It extends standard formats (AnnData, MuData) with GenoAnnData for efficient genotype (via dask) and phenotype (via ehrapy) handling.\n\n![Data structure schematic](docs/_static/img/schematic_figure.png)\n\n````{only} html\n```{image} _static/img/schematic_figure.png\n:width: 750px\n:alt: Data structure schematic\n```\n````\n\n- **Donor-level Data (G):** `GenoAnnData`, Stores individual level data such as genotypes.\n- **Cell-level Data (C):** `AnnData`/ `MuData`, Stores single-cell omics data such as gene expression.\n\nCrucially, **`DonorData`** ensures that genetic data and single-cell modalities remain **synchronized**, preserving their donor-cell pairing even through complex filtering operations (e.g., selecting specific cell types or patient subsets).\n\n### 2. Comprehensive Toolkit\n\n**cellink** offers a streamlined suite of tools for the entire analysis workflow:\n\n- **[Variant Preprocessing \u0026 Annotation](https://cellink-docs.readthedocs.io/en/latest/tutorials/explore_annotations.html):** Tools for quality control, annotation (VCF export/import), and selection of genetic variants.\n- **Specialized Downstream Analysis:** Easily perform complex genetic analyses on single-cell expression data, including:\n    - [eQTL mapping](https://cellink-docs.readthedocs.io/en/latest/tutorials/pseudobulk_eqtl.html).\n    - [Rare variant association studies](https://cellink-docs.readthedocs.io/en/latest/tutorials/burden_testing.html).\n    - [Clumping \u0026 pruning](https://cellink-docs.readthedocs.io/en/latest/tutorials/clumping_pruning.html).\n    - [Colocalization analysis](https://cellink-docs.readthedocs.io/en/latest/tutorials/colocalization.html).\n- **Interoperability:** **cellink** enhances standard workflows through data exports compatible with common genetic analysis\n  tools, e.g., for [eQTL analysis with jaxqtl or tensorqtl](https://cellink-docs.readthedocs.io/en/latest/tutorials/pseudobulk_eqtl_jaxqtl_tensorqtl.html) and includes built-in [dataloaders for deep learning](https://cellink-docs.readthedocs.io/en/latest/tutorials/run_dataloader.html).\n\n## 🚀 Getting Started\n\n- Check out the **[Tutorials](https://cellink-docs.readthedocs.io/en/latest/tutorials/index.html)** section for step-by-step guides on analysis workflows.\n- Explore the **[API Reference](https://cellink-docs.readthedocs.io/en/latest/api/index.html)** for detailed documentation.\n\nInstall the latest development version directly from GitHub:\n\n```bash\npip install git+https://github.com/theislab/cellink.git@main\n```\n\n## Contact\n\n\u003c!-- For questions and help requests, you can reach out in the [scverse discourse][]. --\u003e\n\nIf you found a bug, please use the [issue tracker](https://github.com/theislab/cellink/issues).\n\n## Release notes\n\nt.b.a\n\n\u003c!-- See the [changelog][]. --\u003e\n\n## Citation\n\n\u003e t.b.a\n\n[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge\n[scverse discourse]: https://discourse.scverse.org/\n[issue tracker]: https://github.com/theislab/cellink/issues\n\n\u003c!-- [tests]: https://github.com/theislab/cellink/actions/workflows/test.yml\n[documentation]: https://Single-cell Genetics (Cellink).readthedocs.io\n[changelog]: https://Single-cell Genetics (Cellink).readthedocs.io/en/latest/changelog.html\n[api documentation]: https://Single-cell Genetics (Cellink).readthedocs.io/en/latest/api.html\n[pypi]: https://pypi.org/project/Single-cell Genetics (Cellink) --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fcellink","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fcellink","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fcellink/lists"}