sparty 0.1.0

single-cell in-situ python package

sparty

Spatial analysis for in-situ RNA transcripts in python

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Documentation • Examples • Preprint

Background

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.

Features

• 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

Getting started

Please refer to the documentation. In particular, the

• API documentation.
• Tutorials

Installation

1. Create a conda environment (Python >= 3.11)
2. Install sparty using pip:

conda create -n sparty python==3.11
conda activate sparty
pip install git+https://github.com/cobioda/sparty.git@main

Contribution

If you found a bug or you want to propose a new feature, please use the issue tracker.