scMagnifier – resolving fine-grained cell subtypes via GRN-informed perturbation

• Installation
• Tutorial 1 Using scMagnifier on single-batch datasets
• Tutorial 2 Using scMagnifier on multi-batch datasets
• Tutorial 3 Using scMagnifier on spatial transcriptomic datasets

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Introduction

scMagnifier is designed for identifying fine-grained cell subtypes.
scMagnifier perturbs candidate transcription factors (TFs), propagates perturbation effects through cluster-specific GRNs to simulate post-perturbation expression profiles, and integrates clustering results across multiple perturbations into stable subtype assignments. Additionally, scMagnifier introduces regulatory perturbation consensus UMAP (rpcUMAP), a perturbation-aware visualization that provides clearer separation between cell subtypes and guides the selection of the optimal number of clusters.