semvec/pypi-packages huggingface dataset:
cosmos-dms 1.0.2
Cosmos: A Position-Resolution Causal Model for Direct and Indirect Effects in Protein Functions
License: MIT
Requires Python: >=3.12

# 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.