Getting Started
User Guide
optimize_nicheformer()
calculate_wb_ez()
calculate_niche_density_ratio()
calculate_niche_cluster_membership()
estimate_population_density()
analyze_density_correlation()
analyze_niche_membership()
About
If you use Mievformer in your research, please cite:
[Citation information will be added upon publication]
Banksy: A method for identifying spatial domains in spatial transcriptomics data.
NicheCompass: A tool for identifying cell type niches in spatial omics data.
GraphST: Graph neural network-based spatial transcriptomics analysis.
STAGATE: Spatial-temporal graph attention network for spatial transcriptomics.
PyTorch: Paszke, A., et al. (2019). PyTorch: An Imperative Style, High-Performance Deep Learning Library. NeurIPS.
PyTorch Lightning: Falcon, W., et al. (2019). PyTorch Lightning.
Scanpy: Wolf, F. A., Angerer, P., & Theis, F. J. (2018). SCANPY: large-scale single-cell gene expression data analysis. Genome Biology.
AnnData: Virshup, I., et al. (2021). AnnData: Annotated data.
For questions and feedback, please open an issue on GitHub.