Metadata-Version: 2.1
Name: casanovo
Version: 3.3.0
Summary: De novo mass spectrometry peptide sequencing with a transformer model
Author-email: Melih Yilmaz <melih@cs.washington.edu>, "William E. Fondrie" <fondriew@gmail.com>, Wout Bittremieux <wout.bittremieux@uantwerpen.be>
License: Apache 2.0
Project-URL: Homepage, https://github.com/Noble-Lab/casanovo
Project-URL: Documentation, https://casanovo.readthedocs.io
Project-URL: Bug Tracker, https://github.com/Noble-Lab/casanovo/issues
Project-URL: Discussion Board, https://github.com/Noble-Lab/casanovo/discussions
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: appdirs
Requires-Dist: click
Requires-Dist: depthcharge-ms (<0.2.0,>=0.1.0)
Requires-Dist: natsort
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: psutil
Requires-Dist: PyGithub
Requires-Dist: pytorch-lightning (<2.0,>=1.7)
Requires-Dist: PyYAML
Requires-Dist: requests
Requires-Dist: scikit-learn
Requires-Dist: spectrum-utils
Requires-Dist: tensorboard
Requires-Dist: torch (>=1.9)
Requires-Dist: tqdm
Provides-Extra: dev
Requires-Dist: pre-commit (>=2.7.1) ; extra == 'dev'
Requires-Dist: black (>=19.10b0) ; extra == 'dev'
Requires-Dist: ppx ; extra == 'dev'
Requires-Dist: psims ; extra == 'dev'
Requires-Dist: pyteomics ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Provides-Extra: docs
Requires-Dist: sphinx (>=4.5.0) ; extra == 'docs'
Requires-Dist: myst-parser (>=0.18.1) ; extra == 'docs'
Requires-Dist: sphinx-book-theme (>=0.3.3) ; extra == 'docs'

# Casanovo

**_De Novo_ Mass Spectrometry Peptide Sequencing with a Transformer Model**

![image](https://user-images.githubusercontent.com/32707537/152622912-ca87da20-a64c-4e3f-9ca1-721c6b0d9c64.png)

If you use Casanovo in your work, please cite the following publications:

- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html)
- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *bioRxiv* (2023). [doi:10.1101/2023.01.03.522621](https://doi.org/10.1101/2023.01.03.522621)

## Documentation

#### https://casanovo.readthedocs.io/en/latest/


