Welcome to spacer’s documentation!

spacer (Spatial Analysis of Cellular Engagement and Recruitment) is a multi-instance deep learning framework developed to elucidate the molecular and spatial determinants of cellular recruitment and engagement within tissue microenvironments.

For installation instructions and getting started examples, please see below.

Note

This project is under active development. For questions, feature requests, or contributions, please visit the spacer GitHub repository.

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Documentation Overview

Main Sections

• Installation
  • Setting up the Environment
  • Installing Spacer
• Data Preparation
  • Preprocessing Workflow
  • Required Data Structure
  • Customizing the Mapping
• Quick Start
  • Running Spacer from the Command Line
  • Argument Descriptions
  • Script Overview
  • Example Outputs
  • Tips
• Full User Manual
  • Spacer training Notebook
  • Load reference gene list
  • ── Option A: single AnnData file ───────────────────────────────────────────
  • ── Option B: multi-sample CSV ───────────────────────────────────────────────
  • SPACER Predict Notebook