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Version](https://img.shields.io/pypi/v/grassp)](https://img.shields.io/pypi/v/grassp)\n[![CI](https://github.com/czbiohub-sf/grassp/actions/workflows/CI.yaml/badge.svg)](https://github.com/czbiohub-sf/grassp/actions/workflows/CI.yaml)\n[![docs online](https://img.shields.io/badge/docs-online-blue)](https://public.czbiohub.org/comp.bio/grassp/)\n\n\n[anndata]: https://anndata.readthedocs.io\n[scanpy]: https://scanpy.readthedocs.io\n[protdata]: https://protdata.sf.czbiohub.org\n[documentation]: https://public.czbiohub.org/comp.bio/grassp/\n\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://raw.githubusercontent.com/czbiohub-sf/grassp/refs/heads/main/docs/source/_static/img/logo.svg\" alt=\"grassp logo\" width=\"300\"/\u003e\n\u003c/p\u003e\n\nThe **grassp** (**GR**aph-based **A**nalysis of **S**ubcellular/**S**patial **P**roteomics) python module enables fast, flexible and scalable analysis of subcellular proteomics datasets.\n\nIt uses the [anndata][] format to store mass-spec data and analysis results and [scanpy][] for many of the dimensionality reduction and visualization functions.\n\n**grassp** enables\n\n- Reading the ouput format of most mass-spectrometry search engines (using [protdata][])\n- Calculating subcellular enrichment profiles of proteins for different experimental protocols\n- Annotating the subcellular location of proteins in an unsupervised and semi-supervised manner\n- Detecting proteins at the interface of organelles\n- Detecting multi-localizing proteins (work in progress)\n- Detecting re-localizing proteins between conditions (work in progress)\n- Combining multiple subcellular proteomics datasets\n- Assessing subcellular resolution\n- Finding the optimal experimental design for future experiments based on simulations\n- Integration of multiple modalities (e.g. Lipidomics) (work in progress)\n\nPlease refer to the [documentation] for reference to individual functions and [tutorials](https://public.czbiohub.org/comp.bio/grassp/tutorials/index.html).\n\n## Installation\n\ngrassp can be installed via [pip](https://pypi.org/project/pip/) from [PyPI](https://pypi.org/project/grassp/) with:\n```\npip install grassp\n```\nFor details on installation, please see the [install section of the documentation](https://public.czbiohub.org/comp.bio/grassp/installation.html).\n\n## Changelog\n\nSee the [CHANGELOG.md](https://github.com/czbiohub-sf/grassp/blob/main/CHANGELOG.md) for a detailed history of changes, updates, and version releases.\n\n## Contributing\n\nIf you'd like to contribute to **grassp** please feel free to look at our [contribution guide](https://public.czbiohub.org/comp.bio/grassp/contributing.html) and open a [Pull request](https://github.com/czbiohub-sf/grassp/pulls).\n\n## Authors\n\n**grassp** is created and maintained by the [Computational Biology Platform](https://www.czbiohub.org/comp-biology/) at the [Chan Zuckerberg Biohub San Francisco](https://www.czbiohub.org/sf/). For details, see the [Contributors page](https://public.czbiohub.org/comp.bio/grassp/contributors.html).\n\nTo get in touch please use the [GihHub issues](https://github.com/czbiohub-sf/grassp/issues) page.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fczbiohub-sf%2Fgrassp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fczbiohub-sf%2Fgrassp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fczbiohub-sf%2Fgrassp/lists"}