Spatial proteomics data analysis
This page contains an overview of all the material you need to follow the spatial proteomics data analysis training.
Please note that you have to follow the spatial transcriptomics data analysis training first before you can follow this training.
Software
Data
- Jupyter notebook: run the code to download the Vectra data
- Python script to download the data (store in the same folder as the notebook)
- MacSima data (25 Gb)
Archive
Below you can find the slides archive of the theoretical spatial omics data analysis in 2023 and 2024.
- Analysis of spatial proteomics data (Benjamin Rombaut – Yvan Saeys lab)
Spatial proteomics data analysis
For spatial proteomics data analysis, we use Harpy, another python pipeline that was developed by Benjamin Rombaut from the Saeys Lab. In spatial proteomics you get multiple images, handling all these images is what Harpy is for. It builds on top of Sparrow.