SHA，A toolkit for genomics spatial heterogeneity analysis which is designed for a variety of spatial transcriptomics techniques such as seqFISH+, MERFISH, osmFISH,10X Visium.
SHA provides a series of spatial heterogeneity mining methods, including spatial heterogeneity genes calculation, cell type and tissue area spatial entropy calculation, gene expression regulation network based on geographically weighted regression, spatial accessibility analysis.
We analyzed different datasets from three domains: neurobiology, tumor biology, and developmental biology based on SHA computational frameworks.
There are two ways to use SHA
- git clone https://github.com/Devin-jun/SHA-SpatialHeterogeneityAnalysis.git
- Pip install SpatialHeterogeneityAnalysis
- Pandas
- Numpy
- Scanpy
- Scikit-learn