https://github.com/wanunulab/protein-gd

Data analysis code for Yu et al. (2023) https://doi.org/10.1038/s41587-022-01598-3
https://github.com/wanunulab/protein-gd

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Data analysis code for Yu et al. (2023) https://doi.org/10.1038/s41587-022-01598-3

• Host: GitHub
• URL: https://github.com/wanunulab/protein-gd
• Owner: wanunulab
• License: gpl-3.0
• Created: 2021-08-02T17:12:29.000Z (over 3 years ago)
• Default Branch: master
• Last Pushed: 2023-01-09T20:38:08.000Z (about 2 years ago)
• Last Synced: 2024-11-13T04:35:31.946Z (3 months ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 45.3 MB
• Stars: 1
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# protein-gd

## Data analysis code for [Yu et al. (2023)](https://doi.org/10.1038/s41587-022-01598-3)

### Requirements:

Python >= 3.9

numpy

scipy

matplotlib

tslearn == 0.5.2

scikit-learn 

### Installation:

Simply clone the repository, download the data files, and run through the jupyter notebooks.

### Usage: 

[DTW_Analysis.ipynb](https://github.com/wanunulab/protein-gd/blob/master/DTW_Analysis.ipynb) contains the script for the dynamic time warping analysis of protein translocation unidirectionality.

[GBC_Analysis.ipynb](https://github.com/wanunulab/protein-gd/blob/master/GBC_Analysis.ipynb) contains the script for machine learning classification and discrimination of protein translocation events via a Gradient Boosting Classifier (GBC) model.

## Authors & Credits:

This analysis was written and performed by Ali Fallahi and Amr Makhamreh (Department of Bioengineering, Northeastern University).

The [pypore](https://github.com/jmschrei/PyPore) package was originally written by Jacob Schreiber and Kevin Karplus. We slightly modified it to make it compatible with python 3 and our datafile types.

## Cite us

Please cite this work as:

Yu, L., Kang, X., Li, F. et al. Unidirectional single-file transport of full-length proteins through a nanopore. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-022-01598-3