scispy

scispy#

Single-Cell In-Situ Spatial-Omics Data Analysis

Documentation • Examples • Preprint

Tests Documentation

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

Installation#

  1. Create a conda environment (Python >= 3.10)

  2. Install scispy using pip:

conda create -n scispy python==3.10
conda activate scispy
pip install git+https://github.com/cobioda/scispy.git@main

Contribution#

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

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