Metadata-Version: 2.1
Name: pixelgen-pixelator
Version: 0.14.0
Summary: A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
Home-page: https://github.com/PixelgenTechnologies/pixelator
License: GPL-2.0-only
Keywords: protein,single-cell,molecular-pixelation,spatial,proteomics
Author: Pixelgen Technologies AB
Author-email: developers@pixelgen.com
Maintainer: Alvaro Martinez Barrio
Maintainer-email: alvaro.martinez.barrio@pixelgen.com
Requires-Python: >=3.8,<3.11
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Project-URL: Documentation, https://software.pixelgen.com
Project-URL: Repository, https://github.com/PixelgenTechnologies/pixelator
Description-Content-Type: text/markdown

# Pixelator


![python-version](https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C%203.10-blue)
[![License: GPL v2](https://img.shields.io/badge/License-GPL_v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)

[//]: # (TODO: Enable this once available)
[//]: # (![conda]&#40;https://anaconda.org/bioconda/pixelator/badges/version.svg&#41;)
[//]: # (![pypi]&#40;https://img.shields.io/pypi/v/pixelgen-pixelator&#41;)


[**Documentation**](#documentation) |
[**Installation**](#installation) |
[**Contributing**](#contributing) |
[**Contact**](#contact) |
[**License**](#license) |
[**Credits**](#credits)


Pixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) assays
and analyze PXL data.

It provides the `pixelator` commandline tool to process FASTQ files and generate PXL files and reports
and can be used as a python library for further downstream processing.


<p align="center">
    <img src="https://www.pixelgen.com/wp-content/uploads/2022/12/share-image-pixelgen.png" height=200
     alt="Pixelgen Technologies" />
</p>
<div align="center">© 2023 - Pixelgen Technologies AB</div>

## Documentation

More information about pixelator is available on the [Pixelgen Technologies Software documentation site](https://software.pixelgen.com/).

## Installation

### Installation with pip

Our software pixelator is available on pypi as `pixelgen-pixelator` and can be installed with pip.
It is recommended to install pixelator in a separate virtual environment.

```shell
pip install pixelgen-pixelator
```

### Installation with conda / mamba

A conda package is available on the bioconda channel and can be installed with conda or mamba.

```shell
conda install -c bioconda pixelator
```
or
```shell
mamba install -c bioconda pixelator
```

### Installation from source

You can also install pixelator from source by cloning the repository.

```shell
git clone https://github.com/pixelgentechnologies/pixelator.git
cd pixelator
pip install .
```

### Using docker

The `pixelator` command-line tool can be run with docker images available on
the [GitHub container registry](https://github.com/PixelgenTechnologies/pixelator/pkgs/container/pixelator).

```shell
docker pull ghcr.io/pixelgentechnologies/pixelator:latest
docker run ghcr.io/pixelgentechnologies/pixelator:latest pixelator --help
```

## Contributing

Contribution are welcome!
Please check out the [contributing guidelines](./CONTRIBUTING.md) for more information.

## Contact

For feature requests or bug reports, please use the GitHub [issues](https://github.com/PixelgenTechnologies/pixelator/issues).
For questions, comments, or suggestions you can use the GitHub [discussions](https://github.com/PixelgenTechnologies/pixelator/discussions).

You can also email the development team at [developers@pixelgen.com](mailto:developers@pixelgen.com).

## License

Pixelator is licensed under the [GPL-2.0](./LICENSE) license.

## Credits

Pixelator is developed and maintained by the [developers](https://github.com/PixelgenTechnologies) at [Pixelgen Technologies](https://pixelgen.com).

When using pixelator in your research, please cite the following publication:

> Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, _et al._ “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.


Main development happened thanks to:

- Jose Fernandez Navarro ([@jfnavarro](https://github.com/jfnavarro))
- Alvaro Martinez Barrio ([@ambarrio](https://github.com/ambarrio))
- Johan Dahlberg ([@johandahlberg](https://github.com/johandahlberg))
- Florian De Temmerman ([@fbdtemme](https://github.com/fbdtemme))

A huge thank you to all [code contributors](https://github.com/PixelgenTechnologies/pixelator/graphs/contributors)!

A non-exhaustive list of contributors follows:

- Filip Karlsson ([@fika-pixelgen](https://github.com/fika-pixelgen))
- Max Karlsson ([@maxkarlsson](https://github.com/maxkarlsson))


