https://github.com/theislab/cellink

Scalable framework for integrating single-cell omics with genetic data using AnnData.
https://github.com/theislab/cellink

anndata genetics single-cell

Last synced: 3 months ago
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Scalable framework for integrating single-cell omics with genetic data using AnnData.

• Host: GitHub
• URL: https://github.com/theislab/cellink
• Owner: theislab
• License: apache-2.0
• Created: 2024-08-01T07:07:52.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2026-02-12T17:34:21.000Z (3 months ago)
• Last Synced: 2026-02-13T01:10:44.743Z (3 months ago)
• Topics: anndata, genetics, single-cell
• Language: Python
• Homepage: https://cellink-docs.readthedocs.io/en/latest/index.html
• Size: 9.67 MB
• Stars: 12
• Watchers: 1
• Forks: 2
• Open Issues: 8
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: docs/contributing.md
  • License: LICENSE

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# Single-cell Genetics Package (Cellink)

Welcome to the official documentation for **cellink**—the toolkit designed to bridge the gap between single-cell data and individual-level genetic analysis.

## Motivation

Integrating 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.

## ✨ Key Features & Structure

**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.

![Data structure schematic](docs/_static/img/schematic_figure.png)

````{only} html

```{image} _static/img/schematic_figure.png

:width: 750px

:alt: Data structure schematic

```

````

- **Donor-level Data (G):** `GenoAnnData`, Stores individual level data such as genotypes.

- **Cell-level Data (C):** `AnnData`/ `MuData`, Stores single-cell omics data such as gene expression.

Crucially, **`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).

### 2. Comprehensive Toolkit

**cellink** offers a streamlined suite of tools for the entire analysis workflow:

- **[Variant Preprocessing & 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.

- **Specialized Downstream Analysis:** Easily perform complex genetic analyses on single-cell expression data, including:

    - [eQTL mapping](https://cellink-docs.readthedocs.io/en/latest/tutorials/pseudobulk_eqtl.html).

    - [Rare variant association studies](https://cellink-docs.readthedocs.io/en/latest/tutorials/burden_testing.html).

    - [Clumping & pruning](https://cellink-docs.readthedocs.io/en/latest/tutorials/clumping_pruning.html).

    - [Colocalization analysis](https://cellink-docs.readthedocs.io/en/latest/tutorials/colocalization.html).

- **Interoperability:** **cellink** enhances standard workflows through data exports compatible with common genetic analysis

  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).

## 🚀 Getting Started

- Check out the **[Tutorials](https://cellink-docs.readthedocs.io/en/latest/tutorials/index.html)** section for step-by-step guides on analysis workflows.

- Explore the **[API Reference](https://cellink-docs.readthedocs.io/en/latest/api/index.html)** for detailed documentation.

Install the latest development version directly from GitHub:

```bash

pip install git+https://github.com/theislab/cellink.git@main

```

## Contact

If you found a bug, please use the [issue tracker](https://github.com/theislab/cellink/issues).

## Release notes

t.b.a

## Citation

> t.b.a

[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge

[scverse discourse]: https://discourse.scverse.org/

[issue tracker]: https://github.com/theislab/cellink/issues