A modular, python-based framework for mass spectrometry.
Project description
AlphaStats
An open-source Python package of the AlphaStats ecosystem from the Mann Labs at the Max Planck Institute of Biochemistry. To enable all hyperlinks in this document, please view it at GitHub.
About
An open-source Python package for downstream mass spectrometry data analysis from the Mann Labs at the Max Planck Institute of Biochemistry.
License
AlphaStats was developed by the Mann Labs at the Max Planck Institute of Biochemistry and is freely available with an Apache License. External Python packages (available in the requirements folder) have their own licenses, which can be consulted on their respective websites.
Installation
Pip
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 !:
pip install alphastats
Next, download the AlphaStats repository from GitHub either directly or with a git command. This creates a new alphastats subfolder in your current directory.
git clone https://github.com/MannLabs/alphastats.git
For any Python package, it is highly recommended to use a separate conda virtual environment, as otherwise dependancy conflicts can occur with already existing packages.
conda create --name alphastats python=3.8 -y
conda activate alphastats
Finally, AlphaStats and all its dependancies need to be installed. To take advantage of all features and allow development (with the -e flag), this is best done by also installing the development dependencies instead of only the core dependencies:
pip install -e "./alphastats[development]"
Usage
Python and Jupyter notebooks
AlphaStats can be imported as a Python package into any Python script or notebook with the command import alphastats.
A brief Jupyter notebook tutorial on how to use the API is also present in the nbs folder.
Troubleshooting
In case of issues, check out the following:
- Issues: Try a few different search terms to find out if a similar problem has been encountered before
- Discussions: Check if your problem or feature requests has been discussed before.
Citations
There are currently no plans to draft a manuscript.
How to contribute
If you like this software, you can give us a star to boost our visibility! All direct contributions are also welcome. Feel free to post a new issue or clone the repository and create a pull request with a new branch. For an even more interactive participation, check out the discussions and the the Contributors License Agreement.
Changelog
See the HISTORY.md for a full overview of the changes made in each version.
Release history Release notifications | RSS feed
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Source Distribution
Built Distribution
Hashes for alphastats-0.0.1-py3-none-any.whl
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