A pthon package build on top of spatialdata for Single-Cell In-Situ Spatial-Omics data analysis, developped to handle Vizgen (merscope), Nanostring (cosmx) and 10xGenomics (Xenium) experiments.
- Read in-situ spatial-omics assays experiments: build on top of spatialdata package
- Automatic cell type annotation: scanvi implementation
- Import anatomical .csv shape file from xenium explorer: as anndata observations
- Automatic run pseudobulk data analysis: using decoupler and pydeseq2 packages
- Compute cell type proportion in region: integrating statistical test in case of replicates
- Produce high quality spatial figures: build on top of spatialdata_plot package
Please refer to the documentation. In particular, the
- Create a conda environment (Python >= 3.11)
- Install sparty using pip:
conda create -n sparty python==3.11
conda activate sparty
pip install git+https://github.com/cobioda/sparty.git@mainIf you found a bug or you want to propose a new feature, please use the issue tracker.