A deep learning model for microenvironment estimation based on spatial transcriptomics
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mievformer
mievformer is a Python package for nicheformer analysis, providing tools for spatial transcriptomics data analysis, including niche modeling, cell-cell interaction estimation, and visualization.
Installation
pip install .
Usage
See the tutorial notebook for detailed usage examples.
import mievformer as mf
import scanpy as sc
# Load your data
adata = sc.read_h5ad("path/to/your/data.h5ad")
# Optimize model
adata = mf.optimize_nicheformer(adata, ...)
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