Metadata-Version: 2.4
Name: troutpy
Version: 0.1.0
Summary: Package for the analysis of transcripts outside segmented cells in python
Project-URL: Documentation, https://troutpy.readthedocs.io/
Project-URL: Homepage, https://github.com/sergiomarco25/troutpy
Project-URL: Source, https://github.com/sergiomarco25/troutpy
Author: Sergio Marco Salas
Maintainer-email: Sergio Marco Salas <sergio.salas@helmholtz-munich.de>
License: BSD 3-Clause License
        
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License-File: LICENSE
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
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Description-Content-Type: text/markdown

# troutpy

[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/troutpy/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/troutpy

Package for the analysis of unassigned RNA during segmentation in image-based spatial transcriptomics, in python.

![alt text](images/logo_fish.png)

## Getting started

Please refer to the [documentation][],
in particular, the [API documentation][].

## Installation

You neeed to have Python 3.10 or newer installed on your system.
If you don't have Python installed, we recommend installing [Mambaforge][].

There are several alternative options to install troutpy:

1) Install the latest release of `troutpy` from [PyPI][]:

```bash
pip install troutpy
```

1. Install the latest development version:

```bash
pip install git+https://github.com/theislab/troutpy.git@main
```

## Usage

Please have a look at the [Usage documentation](https://troutpy.readthedocs.io/en/latest/) and the [tutorials](https://troutpy.readthedocs.io/en/latest/).

```python
import troutpy as tp
```

## Reproducibility
Code, notebooks, and instructions to reproduce the results from the paper are available at the [reproducibility repository](https://github.com/theislab/troutpy_reproducibility). This repository also include diverse tutorials and compementary functions that are not core to Troutpy, but are required to reproduce the figures from Marco Salas et al. 2025.

## Release notes

See the [changelog][].

## Contact

For questions and help requests, you can reach out in the [scverse discourse][].
If you found a bug, please use the [issue tracker][].

## Citation

> t.b.a

[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge
[scverse discourse]: https://discourse.scverse.org/
[issue tracker]: https://github.com/theislab/troutpy/issues
[tests]: https://github.com/theislab/troutpy/actions/workflows/test.yml
[documentation]: https://troutpy.readthedocs.io
[changelog]: https://troutpy.readthedocs.io/en/latest/changelog.html
[api documentation]: https://troutpy.readthedocs.io/en/latest/api.html
[pypi]: https://pypi.org/project/troutpy
[images/logo_fish.png]: images/logo_fish.png
