SKNY - Spatial omics analysis tools for tumor microenvironment

SKNY (SpatialKNifeY) is a tools for spatial omics analysis of tumor microenvironment for multiple platform such as Xenium, CosMx, and PhenoCycler. SKNY automatically contours the tumor based on the expression data and calculates the distance from these contours to each coordinate in space. Using this distance data, we provide two analyses:

1. A quantitative evaluation of the peri- and intra-tumoral gene expressions.

2. “Single tumor microenvironment analysis” with bulk gene expression within each contour.

Also, anndata object-based programming makes it compatible with scanpy, squidpy and stlearn.

Documentation

• https://skny.readthedocs.io.

Citation

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