Metadata-Version: 2.4
Name: Statescope
Version: 1.0.6
Summary: Statescope framework to uncover cell states from bulk RNA-seq and DNA-seq data
Author-email: Jurriaan Janssen <j.janssen4@amsterdamumc.nl>, Mischa Steketee <m.f.b.steketee@amsterdamumc.nl>, Aryamaan Bose <a.bose1@amsterdamumc.nl>, Yongsoo Kim <yo.kim@amsterdamumc.nl>
License: MIT License
        
        Copyright (c) 2020 tgac-vumc
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
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        The above copyright notice and this permission notice shall be included in all
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Project-URL: Homepage, https://statescope.netlify.app/
Project-URL: Repository, https://github.com/tgac-vumc/Statescope
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numba
Requires-Dist: numpy<2.0.0
Requires-Dist: scipy
Requires-Dist: scikit-learn
Requires-Dist: joblib
Requires-Dist: pandas<2.0.0
Requires-Dist: statsmodels
Requires-Dist: autogenes>=1.0
Requires-Dist: multiprocess
Requires-Dist: anndata>0.7
Requires-Dist: torch
Requires-Dist: torchvision
Requires-Dist: seaborn
Requires-Dist: requests
Dynamic: license-file

<p align="center">
  <img width="424" height="200" src="https://github.com/tgac-vumc/Statescope/blob/master/img/Logo_Statescope.png">
</p>

# Statescope
Statescope is a computational framework designed to discover cell states from cell type-specific gene expression profiles inferred from bulk RNA profiles.

<p align="center">
  <img width="75%" height="75%" src="https://github.com/tgac-vumc/Statescope/blob/master/img/Statescope_Overview.png">
</p>


## Installation

### Using pip

The python package of Statescope is available on pip:

```
pip install Statescope
```

We tested Statescope with `python => 3.10`.

###  Running a demo script

You can find an basic demo script under the `tutorial` folder.
You can open the script using the command below after installing Statecope:

```
jupyter notebook tutorial/BasicTutorial.ipynb
```

## Documentation

### Website

The documentation of Statescope is hosted on https://tgac-vumc.github.io/Statescopeweb/


## System Requirements

### Hardware Requirements

Statescope can run on the minimal computer spec, such as Binder (1 CPU, 2GB RAM on Google Cloud), when data size is small. However, Statescope can significantly benefit from the larger amount of CPUs and RAM and can leverage GPU hardware.

### OS Requirements

The package development version is tested on Linux operating systems. (CentOS 7 and Ubuntu 16.04). 

