https://github.com/borgwardtlab/maldi_pike

Code for 'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra'
https://github.com/borgwardtlab/maldi_pike

Last synced: 11 months ago
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Code for 'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra'

• Host: GitHub
• URL: https://github.com/borgwardtlab/maldi_pike
• Owner: BorgwardtLab
• License: bsd-3-clause
• Created: 2020-01-31T07:33:44.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2022-04-11T17:58:15.000Z (about 4 years ago)
• Last Synced: 2023-06-29T19:35:30.957Z (almost 3 years ago)
• Language: Python
• Homepage:
• Size: 205 KB
• Stars: 7
• Watchers: 4
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# maldi_PIKE — Peak Information KErnel for MALDI-TOF MS spectra

`maldi_PIKE` is a small library for Python 3 that include the code used for 

'Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass 

spectra'. The main method includes PIKE, the Peak Information KErnel for MALDI-TOF MS spectra, 

embedded in a Gaussian Process. We developed PIKE based on heat diffusion on structured 

objects. It is well suited for MALDI-TOF mass spectra and able to capture interactions between

mass peaks.

# Dependencies

- Python 3.7

- packages listed in `pyproject.toml`

# Installation

- Clone the repository

- `poetry install`

Follow the instructions given by `poetry`.

# Example behaviour of PIKE

Figure 2:

![PIKE_behaviour](PIKE_behaviour.png)

Code to recreate this graphic in matplotlib can be found in

`ismb2020_maldi/visualise_feature_map.py`. Use the script as

follows:

```

poetry run python ismb2020_maldi/visualise_feature_map.py data/Example_peaks.txt

```

This should result in the following plot:

![PIKE_behaviour_matplotlib](PIKE_behaviour_matplotlib.png)

This repository is work in progress.