grassp - Graph-based analysis of subcellular proteomics data#
The grassp (GRaph-based Analysis of Subcellular/Spatial Proteomics) 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.
Installation#
grassp can be installed via pip from PyPI with:
pip install grassp
For details on installation, please see the install section of the documentation.
Contributing#
If you’d like to contribute to grassp please feel free to look at our contribution guide and open a Pull request.