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Name: CIGMA
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======
CIGMA
======


CIMGA is a Python package for the decomposition of cell type-shared and -specific eQTLs using the CIGMA model.
For a full description of CIGMA, please refer to the original paper: https://doi.org/10.1101/2023.08.01.551679.

This repository contains scripts for data analyses in our paper. `Snakemake files <workflow/rules>`_ contain steps for running CIGMA model on simulated and real data.

.. * Download GWAS data from ... and update the path in the [config](config/config.yaml) file.
.. * Download LDSC: git clone https://github.com/bulik/ldsc.git


Installation
============
The conda env is defined in the `environment.yml <env/environment.yml>`_ file.

To create the conda environment, run:

```bash
conda env create -n cigma -f env/environment.yml
conda activate cigma
```


To only install the CIGMA Python package, run:

```bash
pip install cigma
```


To run the tests, run:

```bash
python3 tests/test.py
```


.. _pyscaffold-notes:

Input data
==========
Please check the `test script <tests/test.py>`_ for CIGMA input data and running examples.

Note
====

This project has been set up using PyScaffold 4.4. For details and usage
information on PyScaffold see https://pyscaffold.org/.
