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mbernste / SpatialCorr

SpatialCorr: Identify gene sets with spatially varying correlation
MIT License
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SpatialCorr: Analyzing spatially varying correlation

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About

SpatialCorr is a set of statistical methods for identifying genes whose correlation structure changes across a spatial transcriptomics sample. Along with a set of statistical tests, SpatialCorr also offers a number of methods for visualizing spatially varying correlation.

Here is a schematic overview of the analyses performed by SpatialCorr:

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For more details regarding the underlying method, see the paper:
Bernstein, M.N., Ni, Z., Prasad, A., Brown, J., Mohanty, C., Stewart, R., Newton, M.A., Kendziorski, C. (2022). SpatialCorr: Identifying gene sets with spatially varying correlation structure. Cell Reports Methods.

Installation

To install SpatialCorr using Pip, run the following command:

pip install spatialcorr

Usage

Documentation

For SpatialCorr's API manual, please visit the documentation.

Tutorial

For a tutorial on running SpatialCorr, please see the tutorial. This tutorial can also be run via Google Colab.