Metadata-Version: 2.1
Name: CandyCrunch
Version: 0.1.0
Summary: Package for predicting glycan structure from LC-MS/MS data
Home-page: https://github.com/BojarLab/CandyCrunch
Author: Daniel Bojar
Author-email: daniel.bojar@gu.se
License: UNKNOWN
Description: # CandyCrunch
        
        <img src="./candycrunch_logo.jpg" width="200" />
        
        Predicting glycan structure from LC-MS/MS data, further described in our upcoming manuscript (Urban et al., bioRxiv 2023). If you use `CandyCrunch` or any of our datasets in your project, please cite Urban et al., bioRxiv 2023. The data used to train `CandyCrunch` can be found at Zenodo, under the doi:10.5281/zenodo.7940047
        
        ## Install
        `pip install git+https://github.com/BojarLab/CandyCrunch.git` <br>
        `import CandyCrunch` <br>
        via pip (WIP): <br> `pip install CandyCrunch` <br> `import CandyCrunch`
        
        ## Most important
        `wrap_inference` (in `CandyCrunch.prediction`) <br>
        Wrapper function to predict glycan structures from raw LC-MS/MS spectra using `CandyCrunch`; requires at minimum a filepath/dataframe and the information which glycan class was measured ("N", "O", "lipid", "free", or "other").
        
        `CandyCrumbs` (in `CandyCrunch.analysis`) <br>
        Wrapper function to annotate MSn fragments using `CandyCrumbs`; requires at minimum a hypothesized glycan structure, a list of peak m/z values, and a mass threshold.
        
        ## Modules
        `prediction` <br>
        Contains all the code functionality used in `wrap_inference`. Also contains `process_mzML_stack` to extract spectra from .mzML files <br>
        `analysis` <br>
        Contains all the code functionality used in `CandyCrumbs`. Also contains functions to analyze and compare averaged spectra <br>
        `model` <br>
        Mostly contains code for model definition, dataset handling, and data augmentation; only used in the back-end <br>
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: draw
