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SpatialCorr-sim: Simulate spatial transcriptomics data with spatially varying correlation

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SpatialCorr-Sim: Simulate spatial transcriptomics data

PyPI Version

This package simulates spatial transcriptomics data with spatially varying correlation structure. To do so, it uses a Poisson-lognormal model with parameters inferred from an input dataset.

Here is a schematic overview of the simulation framework:

alt text

Installation

To install SpatialCorr-sim using Pip, run the following command:

pip install spatialcorr-sim

Usage

Documentation

The API manual can be found at https://spatialcorr-sim.readthedocs.io/en/latest/.

Tutorial

For a tutorial on how to simulate a spatial transcriptomics dataset, please see the Jupyter notebook, tutorial/SpatialCorr_sim_tutorial.ipynb.

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