Metadata-Version: 2.3
Name: cosmos-dms
Version: 1.0.2
Summary: Cosmos: A Position-Resolution Causal Model for Direct and Indirect Effects in Protein Functions
License: MIT
Author: Jingyou Rao
Author-email: roseraosh@gmail.com
Requires-Python: >=3.12
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Dist: adjustText
Requires-Dist: arviz (>=0.20,<0.21)
Requires-Dist: matplotlib (>=3.9)
Requires-Dist: numpy (>=2.1,<3.0)
Requires-Dist: pandas (>=2.2,<3.0)
Requires-Dist: scikit-learn (>=1.4,<2.0)
Requires-Dist: scipy (>=1.14,<2.0)
Requires-Dist: seaborn (>=0.13)
Requires-Dist: xarray (>=2024.09,<2025.0)
Description-Content-Type: text/markdown

# Cosmos

<p align="left">
  <img src="https://github.com/pimentellab/cosmos/blob/12bd4a40b079dcde79858287031059013ca42899/cosmos_logo.png" width="150">
</p>

## Update
v1.0: July 15, 2025
- Initial Version of __Cosmos__

## Overview

__Cosmos__ is a Python package for multi-phenotype deep mutational scanning analysis. Specifically, it is suitable for two sequential protein functional phenotypes, one upstream and one downstream - for example, abundance and activity.

## Installation

### `pypi`
```
pip install cosmos-dms
```

### From source

Source code can be found on the GitHub repo [pimentellab/cosmos](https://github.com/pimentellab/cosmos)

__Cosmos__ uses [Poetry](https://python-poetry.org/) for environment and dependency management.

To install __Cosmos__, follow these steps:
1. Install Poetry (if not already installed). Please follow the guideline on [Poetry's official documentation](https://python-poetry.org/docs/).
2. Clone the repository.
```{bash}
git clone https://github.com/pimentellab/cosmos.git
cd cosmos
```
3. Install and activate the environment.
```{bash}
poetry lock
poetry install
```

## Getting started

Check out the `vignette/` directory in the source code.




