Repository for Nicheformer: a foundation model for single-cell and spatial omics

Federated Fine-Tuning and Zero Shot Application of Nicheformers for Spatial Transcriptomics

Leveraging the Unity3D engine and the Nicheformer foundation model, this system builds a digital twin platform for spatial transcriptomics. It reconstructs cellular spatial relationships in virtual space, capturing local micro-environmental details and spatial continuity that static charts fail to reveal.

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Analysis capsule for nicheformer LC-NE data

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NicheFormer: A Spatial Graph Transformer and Causal Inference Framework Decodes COL1A1-Driven Desmoplasia and Evolutionary Dynamics in Human Breast Carcinoma

Using NicheFormer to develop a spatially aware single cell model

This repository contains code for systematic comparison of foundation models and classical feature representation methods for spatial transcriptomics analysis. We evaluate scGPT, Geneformer, Nicheformer and Novae, against classical methods such as PCA, NMF and CoCo-ST across core spatial-omics tasks.