Metadata-Version: 2.1
Name: alphastats
Version: 0.2.3
Summary: An open-source Python package for Mass Spectrometry Analysis
Home-page: https://github.com/MannLabs/alphastats
Author: Mann Labs
Author-email: elena.krismer@hotmail.com
License: Apache
Project-URL: Mann Labs at MPIB, https://www.biochem.mpg.de/mann
Project-URL: GitHub, https://github.com/MannLabs/alphastats
Project-URL: ReadTheDocs, https://mannlabs.github.io/alphastats/
Project-URL: PyPi, https://pypi.org/project/alphastats/
Keywords: bioinformatics,software,mass spectometry
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7,<4
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: pandas
Requires-Dist: scikit-learn
Requires-Dist: data-cache
Requires-Dist: plotly
Requires-Dist: iteration-utilities
Requires-Dist: openpyxl
Requires-Dist: sklearn-pandas
Requires-Dist: pingouin
Requires-Dist: scipy
Requires-Dist: tqdm
Requires-Dist: diffxpy
Requires-Dist: anndata
Requires-Dist: umap-learn
Requires-Dist: streamlit
Provides-Extra: development
Requires-Dist: jupyter ; extra == 'development'
Requires-Dist: jupyter-contrib-nbextensions ; extra == 'development'
Requires-Dist: pyinstaller ; extra == 'development'
Requires-Dist: autodocsumm ; extra == 'development'
Requires-Dist: sphinx-rtd-theme ; extra == 'development'
Requires-Dist: twine ; extra == 'development'
Requires-Dist: bumpversion ; extra == 'development'
Requires-Dist: pipdeptree ; extra == 'development'
Requires-Dist: ipykernel ; extra == 'development'
Requires-Dist: tqdm ; extra == 'development'
Requires-Dist: psutil ; extra == 'development'
Provides-Extra: development-stable
Requires-Dist: jupyter ; extra == 'development-stable'
Requires-Dist: jupyter-contrib-nbextensions ; extra == 'development-stable'
Requires-Dist: pyinstaller ; extra == 'development-stable'
Requires-Dist: autodocsumm ; extra == 'development-stable'
Requires-Dist: sphinx-rtd-theme ; extra == 'development-stable'
Requires-Dist: twine ; extra == 'development-stable'
Requires-Dist: bumpversion ; extra == 'development-stable'
Requires-Dist: pipdeptree ; extra == 'development-stable'
Requires-Dist: ipykernel ; extra == 'development-stable'
Requires-Dist: tqdm ; extra == 'development-stable'
Requires-Dist: psutil ; extra == 'development-stable'
Provides-Extra: gui
Requires-Dist: streamlit ; extra == 'gui'
Requires-Dist: streamlit-multipage ; extra == 'gui'
Provides-Extra: gui-stable
Requires-Dist: streamlit (>=1.12.2) ; extra == 'gui-stable'
Requires-Dist: streamlit-multipage (>=0.0.18) ; extra == 'gui-stable'
Provides-Extra: stable
Requires-Dist: pandas (>=1.4.2) ; extra == 'stable'
Requires-Dist: scikit-learn ; extra == 'stable'
Requires-Dist: data-cache (>=0.1.6) ; extra == 'stable'
Requires-Dist: plotly (>=5.7.0) ; extra == 'stable'
Requires-Dist: iteration-utilities ; extra == 'stable'
Requires-Dist: openpyxl (>=3.0.10) ; extra == 'stable'
Requires-Dist: sklearn-pandas (>=2.2.0) ; extra == 'stable'
Requires-Dist: pingouin (>=0.5.2) ; extra == 'stable'
Requires-Dist: scipy (>=1.8.1) ; extra == 'stable'
Requires-Dist: tqdm (>=4.64.0) ; extra == 'stable'
Requires-Dist: diffxpy (>=0.7.4) ; extra == 'stable'
Requires-Dist: anndata (>=0.8.0) ; extra == 'stable'
Requires-Dist: umap-learn (>=0.5.3) ; extra == 'stable'
Requires-Dist: streamlit (>=1.12.2) ; extra == 'stable'

[![codecov](https://codecov.io/gh/MannLabs/alphastats/branch/main/graph/badge.svg?token=HY4A0KKLRI)](https://codecov.io/gh/MannLabs/alphastats)


<p align="center">
  <img src="https://github.com/MannLabs/alphapeptstats/blob/main/alphastats/gui/alphapeptstats_logo.png?raw=true" />
</p>


An open-source Python package of the AlphaPept ecosystem from the [Mann Group at the University of Copenhagen](https://www.biochem.mpg.de/mann).

The full documentation can be found [here](https://alphapeptstats.readthedocs.io/en/latest/).

* [**About**](#about)
* [**Installation**](#installation)
* [**Usage**](#usage)
* [**Troubleshooting**](#troubleshooting)
* [**Citations**](#citations)
* [**License**](#license)
* [**How to contribute**](#how-to-contribute)
* [**Changelog**](#changelog)

---
## About
An open-source Python package for downstream mass spectrometry downstream data analysis from the [Mann Group at the University of Copenhagen](https://www.cpr.ku.dk/research/proteomics/mann/).

---

## Installation

AlphaStats can be installed in an existing Python 3.8 environment with a single `bash` command. *This `bash` command can also be run directly from within a Jupyter notebook by prepending it with a `!`*:

```bash
pip install alphastats
```
---
## Usage

For the Graphical User Interface
 
```bash
alphastats gui
```

AlphaStats can be imported as a Python package into any Python script or notebook with the command `import alphastats`.

A brief [Jupyter notebook tutorial](nbs/workflow_mq.ipynb) on how to use the API is also present in the [nbs folder](nbs).

---

## GUI
![Screenshot 2023-01-05 at 17 15 46](https://user-images.githubusercontent.com/70535771/210976707-f6b8daa8-f6e9-4177-a01f-c18df37c4bec.png)

![Screenshot 2023-01-05 at 17 23 51](https://user-images.githubusercontent.com/70535771/210976730-af59c3bf-d092-4cc1-8de8-212fce9e6faa.png)


## Troubleshooting

In case of issues, check out the following:

* [Issues](https://github.com/MannLabs/alphapeptstats/issues): Try a few different search terms to find out if a similar problem has been encountered before
* [Discussions](https://github.com/MannLabs/alphapeptstats/discussions): Check if your problem or feature requests has been discussed before.

---
## License

AlphaStats was developed by the [Mann Group at the University of Copenhagen](https://www.cpr.ku.dk/research/proteomics/mann/) and is freely available with an [Apache License](LICENSE.txt). External Python packages (available in the [requirements](requirements) folder) have their own licenses, which can be consulted on their respective websites.

---
## How to contribute

If you like this software, you can give us a [star](https://github.com/MannLabs/alphapeptstats/stargazers) to boost our visibility! All direct contributions are also welcome. Feel free to post a new [issue](https://github.com/MannLabs/alphapeptstats/issues) or clone the repository and create a [pull request](https://github.com/MannLabs/alphapeptstats/pulls) with a new branch. For an even more interactive participation, check out the [discussions](https://github.com/MannLabs/alphapeptstats/discussions) and the [the Contributors License Agreement](misc/CLA.md).

---
## Changelog

See the [HISTORY.md](HISTORY.md) for a full overview of the changes made in each version.
