SDEvelo Documentation

Welcome to the SDEvelo documentation! SDEvelo represents a significant advancement in single-cell RNA sequencing (scRNA-seq) and sequence-based spatial transcriptomics (ST) analysis.

Contents

• Overview of SDEvelo
  • SDEvelo: A Deep Generative Approach for Transcriptional Dynamics
  • Workflow and Downstream Analysis
  • Key Features
  • Addressing Limitations in Existing Methods
  • SDEvelo’s Unique Approach
• Installation Guide
  • System Requirements
  • Dependencies
  • Installation Steps
  • Installing from Source
  • GPU Support
  • Troubleshooting

Key Features

• Multivariate stochastic modeling of transcriptional dynamics

• Cell-specific latent time estimation

• Versatile Compatibility: Applicable to both scRNA-seq and sequencing-based spatial transcriptomics data

• Computationally Scalable

Quick Start

To install SDEvelo, use pip:

pip install sdevelo

For more detailed usage instructions, see the Installation section.

Tutorials

Explore our comprehensive tutorials to get started with SDEvelo:

Tutorials

• Simulation Tutorial
• HCC section 1
• HCC section 2
• Reprogramming demo
• Erythroid Differentiation Tutorial
• PBMCs demo