Metadata-Version: 2.2
Name: cascadia
Version: 0.0.6
Summary: De novo sequencing for DIA mass spectrometry data
Author-email: Justin Sanders <jsander1@uw.edu>
Project-URL: Homepage, https://github.com/Noble-Lab/cascadia
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: lightning<2.1,>=2.0
Requires-Dist: pytorch-lightning<2.0,>=1.9
Requires-Dist: pyteomics>=4.6
Requires-Dist: torch<2.1,>=2.0
Requires-Dist: numpy<2.0
Requires-Dist: numba>=0.48.0
Requires-Dist: lxml>=4.9.1
Requires-Dist: h5py>=3.7.0
Requires-Dist: einops>=0.4.1
Requires-Dist: tqdm>=4.65.0
Requires-Dist: lark>=1.1.4
Requires-Dist: selfies>=2.1.1
Requires-Dist: sortedcontainers>=2.4.0
Requires-Dist: dill>=0.3.6
Requires-Dist: rdkit>=2023.03.1
Requires-Dist: pillow>=9.4.0
Requires-Dist: spectrum-utils>=0.4.1
Requires-Dist: tensorboard

# Cascadia


**A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data**

![image](docs/source/cascadia-graphical-abstract.png)

If you use Cascadia in your work, please cite the following publication:

Sanders, Justin, et al. ‘A Transformer Model for de Novo Sequencing of Data-Independent Acquisition Mass Spectrometry Data’. bioRxiv, Cold Spring Harbor Laboratory, 2024, [https://doi.org/10.1101/2024.06.03.597251](https://doi.org/10.1101/2024.06.03.597251).

## Documentation

Documentation for Cascadia is avaialable at:
[https://cascadia.readthedocs.io/en/latest/index.html](https://cascadia.readthedocs.io/en/latest/index.html)
