🆔sc-suite

A suite of tools for identifiable single-cell / spatial data analysis, including:

• SIMVI: Spatial Interaction Modeling using Variational Inference

• scShift: Scaling deep identifiable models enables zero-shot characterization of single-cell biological states

Installation

• Installation
  • Install SIMVI
  • Install scShift

API

• SIMVI
  • SimVI Model
• scShift API
  • Overview

Tutorials

• SIMVI tutorial on MERFISH MTG data
  • Import packages
  • Import and preprocess datasets
  • Run SIMVI model
  • Spatial effect analysis
• scShift tutorial on blood data
  • Load trained scShift model
  • Train a scShift model from scratch
  • Zero-shot analysis by scShift