Metadata-Version: 2.4
Name: poreflow
Version: 0.4.5
Summary: Python module for processing nanopore sequencing
Author-email: Xiuqi Chen <X.Chen-13@tudelft.nl>, Thijn Hoekstra <thijnhoekstra@gmail.com>
License: MIT License
        
        Copyright (c) [2025] [Xiuqi Chen]
        
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Project-URL: Repository, https://gitlab.tudelft.nl/xiuqichen/poreFlow.git
Project-URL: Issues, https://gitlab.tudelft.nl/xiuqichen/poreFlow/-/issues
Keywords: nanopore,peptide,bioinformatics
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE.MD
Requires-Dist: numpy>=2.2.6
Requires-Dist: scipy>=1.15.3
Requires-Dist: tqdm>=4.67.1
Requires-Dist: pandas>=2.3.1
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Requires-Dist: matplotlib>=3.10.5
Requires-Dist: plotly>=6.2.0
Requires-Dist: h5py>=3.14.0
Requires-Dist: seaborn>=0.13.2
Requires-Dist: dash>=4.1.0
Requires-Dist: dash-bootstrap-components>=1.6.0
Requires-Dist: psutil>=7.1.3
Requires-Dist: dash-ag-grid>=33.3.3
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Requires-Dist: pydantic>=2.12.5
Requires-Dist: plotly-resampler>=0.10.0
Requires-Dist: pytz
Requires-Dist: ipython>=9.10.1
Dynamic: license-file

# PoreFlow
> *Nanopore data analysis tools*

[![pipeline status](https://gitlab.tudelft.nl/xiuqichen/poreFlow/badges/main/pipeline.svg)](https://gitlab.tudelft.nl/xiuqichen/poreFlow/-/commits/main)
[![Latest Release](https://gitlab.tudelft.nl/xiuqichen/poreFlow/-/badges/release.svg)](https://gitlab.tudelft.nl/xiuqichen/poreFlow/-/releases)

PoreFlow is a fast, simple, and flexible set of tools for analysing raw nanopore sequencing data, 
intended for use for research in the Cees Dekker lab (and beyond?). 

Please see the [Documentation][PoreFlow] for an introductory tutorial and full user guide.

## Features

- Python API for storing measurement, event, and step data.
- Event detection algorithm
- Fast step detection algorithm written in C++
- Support for reasarch .fast5 files, along with .dat files from the UTube device
- Filter events with basic metrics and store metadata
- Find DNA-peptide boundary with expected DNA sequence

## If you need help with PoreFlow, do not hesitate to get in contact:
- For questions, contact the authors in-person or via email
- To report a bug or make a feature request, open an **[Issue]** on GitLab.

## Links
- [Official Documentation][PoreFlow]

## Contributing to PoreFlow
Please see the [Contributing Guide] for information on how you can help develop PoreFlow.


## Authors
Thijn Hoekstra, Xiuqi Chen

## License
[MIT license](https://gitlab.tudelft.nl/xiuqichen/poreFlow/LICENSE)

<!-- Links -->
[PoreFlow]: https://twhoekstra.github.io/poreFlow-docs/
[Issue]: https://https://gitlab.tudelft.nl/xiuqichen/poreFlow/issues
[Contributing Guide]: https://twhoekstra.github.io/poreFlow-docs/contributing/
[PyPA Code of Conduct]: https://www.pypa.io/en/latest/code-of-conduct/
