SpatialQuery is a package for fast query of Spatial Transcriptomics data.

Analysis of ST data in SpatialQuery

With annotated ST data as input, SpatialQuery first builds a k-D tree based on spatial location in each FOV for fast query of neighboring cell compositions. It is composed of methods for single-FOV and multiple-FOVs. In single-FOV, it contains methods:

• identify frequent patterns across FOV
• identify frequent patterns around cell type of interest
• identify statistically significant patterns around cell type of interest

For multiple-FOVs data, it contains methods:

• identify frequent patterns around cell type of interest in specified datasets
• identify statistically significant patterns around cell type of interest in specified datasets
• identify differential patterns across datasets

Installation

pip install -i https://test.pypi.org/simple/ SpatialQuery

For more details, please refer to examples/SpatialQuery-example.ipynb.