[](https://badge.fury.io/py/alphastats)
[](https://codecov.io/gh/MannLabs/alphastats)
[](https://pepy.tech/project/alphastats)
[](https://pepy.tech/project/alphastats)
[](https://github.com/MannLabs/alphapeptstats/actions/workflows/python-package.yml)
[](https://alphapeptstats.readthedocs.io/en/latest/?badge=latest)
<div align = center>
<img src="https://github.com/MannLabs/alphapeptstats/blob/main/misc/alphastats_workflow.png?raw=true" width="771.4" height="389.2">
</div>
<div align = center>
<br>
<br>
[<kbd> <br> Documentation <br> </kbd>][link]
</div>
<br>
<br>
[link]:https://alphapeptstats.readthedocs.io/en/main/
<div align = center>
<br>
<br>
[<kbd> <br> Streamlit WebApp <br> </kbd>][link_streamlit]
</div>
<br>
<br>
[link_streamlit]:https://mannlabs-alphapeptstats-alphastatsguialphapeptstats-qyzgwd.streamlit.app/
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/).
* [**Citation**](#citation)
* [**Installation**](#installation)
* [**Troubleshooting**](#troubleshooting)
* [**License**](#license)
* [**How to contribute**](#how-to-contribute)
* [**Changelog**](#changelog)
---
## Citation
Publication: [AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics](https://doi.org/10.1093/bioinformatics/btad461)
> **Citation:** <br>
> Krismer, E., Bludau, I., Strauss M. & Mann M. (2023). AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics. Bioinformatics
> https://doi.org/10.1093/bioinformatics/btad461
---
## Installation
AlphaPeptStats can be used as
* python library (pip-installation), or
* Graphical User Interface (either pip-installation or one-click installer).
Further we provide a Dockerimage for the GUI.
### Pip Installation
AlphaStats can be installed in an existing Python 3.8/3.9/3.10 environment with a single `bash` command.
```bash
pip install alphastats
```
In case you want to use the Graphical User Interface, use following command in the command line:
```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/getting_started.ipynb) on how to use the API is also present in the [nbs folder](nbs).
### One Click Installer
One click Installer for MacOS, Windows and Linux can be found [here](https://github.com/MannLabs/alphapeptstats/releases).
### Docker Image
We provide two Dockerfiles, one for the library and one for the Graphical User Interface.
The Image can be pulled from Dockerhub
```bash
docker pull elenakrismer/alphapeptstats_streamlit
```
---
## GUI
---
## 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
---
## 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.
---
## FAQ
### How can I resolve the Microsoft visual error message when installing: error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools"?
Please, find a description on how to update required tools [here](https://github.com/MannLabs/alphapeptstats/issues/158).
## How to resolve ERROR:: Could not find a local HDF5 installation. on Mac M1?
Before installing AlphaPeptStats you might need to install pytables first:
````
conda install -c anaconda pytables
````
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