{"id":46436070,"url":"https://github.com/pixelgentechnologies/pixelator","last_synced_at":"2026-05-29T13:00:48.673Z","repository":{"id":194804567,"uuid":"691087753","full_name":"PixelgenTechnologies/pixelator","owner":"PixelgenTechnologies","description":"A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.","archived":false,"fork":false,"pushed_at":"2026-05-26T14:59:34.000Z","size":87190,"stargazers_count":20,"open_issues_count":6,"forks_count":4,"subscribers_count":4,"default_branch":"dev","last_synced_at":"2026-05-26T16:34:40.961Z","etag":null,"topics":["molecular-pixelation","pixelgen-technologies","protein","proteomics","proximity-network","single-cell","single-cell-omics","spatial"],"latest_commit_sha":null,"homepage":"https://pixelgen.com","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PixelgenTechnologies.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-09-13T13:28:14.000Z","updated_at":"2026-05-26T09:45:34.000Z","dependencies_parsed_at":"2023-09-25T20:14:57.693Z","dependency_job_id":"94bb051e-355c-443f-beef-39f1ea8e40fd","html_url":"https://github.com/PixelgenTechnologies/pixelator","commit_stats":{"total_commits":219,"total_committers":9,"mean_commits":"24.333333333333332","dds":0.4292237442922374,"last_synced_commit":"101e329f2ec28b2f1fbfc5a7722099c4f18828ea"},"previous_names":["pixelgentechnologies/pixelator"],"tags_count":33,"template":false,"template_full_name":null,"purl":"pkg:github/PixelgenTechnologies/pixelator","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PixelgenTechnologies%2Fpixelator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PixelgenTechnologies%2Fpixelator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PixelgenTechnologies%2Fpixelator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PixelgenTechnologies%2Fpixelator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PixelgenTechnologies","download_url":"https://codeload.github.com/PixelgenTechnologies/pixelator/tar.gz/refs/heads/dev","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PixelgenTechnologies%2Fpixelator/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33652986,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-05-29T02:00:06.066Z","response_time":107,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["molecular-pixelation","pixelgen-technologies","protein","proteomics","proximity-network","single-cell","single-cell-omics","spatial"],"created_at":"2026-03-05T21:06:57.477Z","updated_at":"2026-05-29T13:00:48.667Z","avatar_url":"https://github.com/PixelgenTechnologies.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Pixelator\n\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pixelgen-pixelator)\n[![MIT](https://img.shields.io/badge/license-MIT-blue)](https://opensource.org/licenses/MIT)\n[![DOI](https://img.shields.io/badge/DOI-10.1038/S41592--024--02268--9-B31B1B.svg)](https://doi.org/10.1038/s41592-024-02268-9)\n[![conda](https://anaconda.org/bioconda/pixelator/badges/version.svg)](https://bioconda.github.io/recipes/pixelator/README.html#package-pixelator)\n[![pypi](https://img.shields.io/pypi/v/pixelgen-pixelator)](https://pypi.org/project/pixelgen-pixelator/)\n[![Docker Repository on Quay](https://quay.io/repository/pixelgen-technologies/pixelator/status \"Docker Repository on Quay\")](https://quay.io/repository/pixelgen-technologies/pixelator)\n[![Tests](https://github.com/PixelgenTechnologies/pixelator/actions/workflows/tests.yml/badge.svg)](https://github.com/PixelgenTechnologies/pixelator/actions/workflows/tests.yml)\n\n[**Documentation**](#documentation) |\n[**Installation**](#installation) |\n[**Usage**](#usage) |\n[**Contributing**](#contributing) |\n[**Contact**](#contact) |\n[**License**](#license) |\n[**Credits**](#credits)\n\nPixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) and\nProximity Network (PNA) assays and analyze PXL data.\n\nIt provides the `pixelator` commandline tool to process FASTQ files and generate PXL files and reports\nand can be used as a python library for further downstream processing.\n\n\u003cp align=\"center\"\u003e\n    \u003cimg src=\"https://www.pixelgen.com/wp-content/uploads/2022/12/share-image-pixelgen.png\" height=200\n     alt=\"Pixelgen Technologies\" /\u003e\n\u003c/p\u003e\n\u003cdiv align=\"center\"\u003e© 2023 - Pixelgen Technologies AB\u003c/div\u003e\n\n## Documentation\n\nMore information about pixelator is available on the [Pixelgen Technologies Software documentation site](https://software.pixelgen.com/).\n\n## Installation\n\nPixelgen Technologies has developed and tested pixelator extensively in Ubuntu 20.04.6 LTS. However, pixelator should run on computers installed with any recent version of the major Linux distributions.\n\nPixelator is available on PyPi as `pixelgen-pixelator` and can be installed with pip. It is recommended to install pixelator in a separate virtual environment.\n\n```shell\npip install pixelgen-pixelator\n```\n\n### Additional installation instructions\n\nFor runnning some of the MPX related pixelator commands you will need to have `fastp` installed on\nyou system. For installation instructions, please visit the [fastp GitHub repository](https://github.com/OpenGene/fastp).\n\n### Installation from source\n\nYou can also install pixelator from source by cloning the repository.\n\n```shell\ngit clone https://github.com/pixelgentechnologies/pixelator.git\ncd pixelator\npip install .\n```\n\n### Using docker\n\nThe `pixelator` command-line tool can be run with docker images available on\nthe [Quay container registry](https://quay.io/repository/pixelgen-technologies/pixelator).\n\n```shell\ndocker pull quay.io/pixelgen-technologies/pixelator:latest\ndocker run quay.io/pixelgen-technologies/pixelator:latest pixelator --help\n```\n\n## Usage\n\nOur recommendation is to use pixelator via the specific Nextflow pipeline, [nf-core/pixelator](https://github.com/nf-core/pixelator).\n\nIt should take only a few seconds to download the pipeline and approx. 20 min to run the default test dataset in a normal commodity computer.\n\nHowever, with MPX data, we recommend running pixelator in specialized hardware with at least 32GB RAM.\n\n## Contributing\n\nContribution are welcome!\nPlease check out the [contributing guidelines](./CONTRIBUTING.md) for more information.\n\n## Contact\n\nFor feature requests or bug reports, please use the GitHub [issues](https://github.com/PixelgenTechnologies/pixelator/issues).\nFor questions, comments, or suggestions you can use the GitHub [discussions](https://github.com/PixelgenTechnologies/pixelator/discussions).\n\nYou can also email the development team at [developers@pixelgen.com](mailto:developers@pixelgen.com).\n\n## License\n\nPixelator is licensed under the [MIT](./LICENSE) license.\n\n## Credits\n\nPixelator is developed and maintained by the [developers](https://github.com/PixelgenTechnologies) at [Pixelgen Technologies](https://pixelgen.com).\n\nWhen using pixelator in your research, please cite the following publication if you are working with Proximity Network Assay data:\n\n\u003e Filip Karlsson, Michele Simonetti, Christina Galonska, Max Karlsson, Hanna van Ooijen, Tomasz Kallas, Divya Thiagarajan, _et al._. \"Single-Cell Protein Interactomes by the Proximity Network Assay\". bioRxiv 2025.06.19.660329; doi: https://doi.org/10.1101/2025.06.19.660329\n\nAnd for Molecular Pixelation data, please cite:\n\n\u003e Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, _et al._ \"Molecular pixelation: spatial proteomics of single cells by sequencing.\" Nature Methods, May 8, 2024. https://doi.org/10.1038/s41592-024-02268-9.\n\nMain development happened thanks to:\n\n- Jose Fernandez Navarro ([@jfnavarro](https://github.com/jfnavarro))\n- Alvaro Martinez Barrio ([@ambarrio](https://github.com/ambarrio))\n- Johan Dahlberg ([@johandahlberg](https://github.com/johandahlberg))\n- Florian De Temmerman ([@fbdtemme](https://github.com/fbdtemme))\n\nA huge thank you to all [code contributors](https://github.com/PixelgenTechnologies/pixelator/graphs/contributors)!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpixelgentechnologies%2Fpixelator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpixelgentechnologies%2Fpixelator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpixelgentechnologies%2Fpixelator/lists"}