https://github.com/czbiohub-sf/grassp

GRaph-based Analysis of Subcellular/Spatial Proteomics
https://github.com/czbiohub-sf/grassp

anndata proteomics-data-analysis scanpy spatial-proteomics subcellular-localization

Last synced: 4 months ago
JSON representation

GRaph-based Analysis of Subcellular/Spatial Proteomics

• Host: GitHub
• URL: https://github.com/czbiohub-sf/grassp
• Owner: czbiohub-sf
• License: bsd-3-clause
• Created: 2024-09-02T18:04:17.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2026-02-02T19:15:36.000Z (4 months ago)
• Last Synced: 2026-02-03T03:32:49.591Z (4 months ago)
• Topics: anndata, proteomics-data-analysis, scanpy, spatial-proteomics, subcellular-localization
• Language: Python
• Homepage: https://public.czbiohub.org/comp.bio/grassp/
• Size: 1.26 MB
• Stars: 7
• Watchers: 2
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md
  • Authors: AUTHORS

Awesome Lists containing this project

README

          
[![PyPI - Version](https://img.shields.io/pypi/v/grassp)](https://img.shields.io/pypi/v/grassp)

[![CI](https://github.com/czbiohub-sf/grassp/actions/workflows/CI.yaml/badge.svg)](https://github.com/czbiohub-sf/grassp/actions/workflows/CI.yaml)

[![docs online](https://img.shields.io/badge/docs-online-blue)](https://public.czbiohub.org/comp.bio/grassp/)

[anndata]: https://anndata.readthedocs.io

[scanpy]: https://scanpy.readthedocs.io

[protdata]: https://protdata.sf.czbiohub.org

[documentation]: https://public.czbiohub.org/comp.bio/grassp/



  



The **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.

It uses the [anndata][] format to store mass-spec data and analysis results and [scanpy][] for many of the dimensionality reduction and visualization functions.

**grassp** enables

- Reading the ouput format of most mass-spectrometry search engines (using [protdata][])

- Calculating subcellular enrichment profiles of proteins for different experimental protocols

- Annotating the subcellular location of proteins in an unsupervised and semi-supervised manner

- Detecting proteins at the interface of organelles

- Detecting multi-localizing proteins (work in progress)

- Detecting re-localizing proteins between conditions (work in progress)

- Combining multiple subcellular proteomics datasets

- Assessing subcellular resolution

- Finding the optimal experimental design for future experiments based on simulations

- Integration of multiple modalities (e.g. Lipidomics) (work in progress)

Please refer to the [documentation] for reference to individual functions and [tutorials](https://public.czbiohub.org/comp.bio/grassp/tutorials/index.html).

## Installation

grassp can be installed via [pip](https://pypi.org/project/pip/) from [PyPI](https://pypi.org/project/grassp/) with:

```

pip install grassp

```

For details on installation, please see the [install section of the documentation](https://public.czbiohub.org/comp.bio/grassp/installation.html).

## Changelog

See the [CHANGELOG.md](https://github.com/czbiohub-sf/grassp/blob/main/CHANGELOG.md) for a detailed history of changes, updates, and version releases.

## Contributing

If 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).

## Authors

**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).

To get in touch please use the [GihHub issues](https://github.com/czbiohub-sf/grassp/issues) page.