<details>
<summary>Table of Contents</summary>
<ol>
<li>
<a href="#package-description">Package description</a>
<ul>
</ul>
</li>
<li>
<a href="#getting-started">Getting Started</a>
<ul>
</ul>
</li>
<li><a href="#usage">Usage</a></li>
<li><a href="#contributing">Contributing</a></li>
<li><a href="#license">License</a></li>
</details>
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## Package description
Introducing Proteomics Downstream Analysis v0.1.0, a comprehensive Python package designed to simplify and streamline the process of downstream data analysis for proteomics research. This package offers a user-friendly and efficient way to handle, manipulate, process, and visualize large proteomics datasets, helping researchers gain valuable insights from their data more quickly and effectively.
Key features of proteomics_downstream_analysis v0.1.0 include:
Data import and preprocessing: Easily import and preprocess raw proteomics data from DIA-NN. Automatically handle missing values, normalization, and data transformation as needed.
Statistical analysis: Perform essential statistical tests such as t-tests, ANOVA, and multiple testing correction methods to assess the significance of differentially expressed proteins.
Enrichment analysis: Conduct functional enrichment analysis to identify over-represented functional categories, biological processes, or pathways in your protein sets, supporting popular databases like Gene Ontology and KEGG.
Clustering and dimensionality reduction: Apply advanced unsupervised learning techniques to group similar proteins and uncover underlying biological patterns. Techniques include hierarchical clustering, k-means clustering, principal component analysis (PCA), and t-distributed stochastic neighbor embedding (t-SNE).
Customizable data visualization: Create stunning and informative visualizations to better understand and communicate your results. Generate heatmaps, volcano plots, Venn diagrams, and more with full customization options.
Integration with existing tools: Compatibility with popular Python libraries including NumPy, pandas, and matplotlib, allowing you to seamlessly integrate this package into your existing data analysis workflow.
Proteomics Downstream Analysis v0.1.0 provides a solid foundation for your proteomics research needs.
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## Getting Started
ProteomicsDownstreamAnalysis can be installed using:
```
pip install proteomics-downstream-analysis
```
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## Usage
```
import proteomics_downstream_analysis as pda
```
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## Contributing
Contribution is much appreciated. Happy to get feedback and suggestions!
Should you have a suggestion that could enhance this project, kindly fork the repository and create a pull request. You may also open an issue labeled as “improvement”.
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## License
Distributed under the MIT License. See `MIT.txt` for more information.
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