Welcome to the GraphVelo documentation.

GraphVelo is a graph-based machine learning procedure that uses RNA velocities inferred from existing methods as input and infers velocity vectors lie in the tangent space of the low-dimensional manifold formed by the single cell data.

Key Features

• Refine the velocity vectors estimated by any methods (e.g. splicing-based, metabolic labeling-based, pseudotime-based, lineage tracing-based etc.) to the data manifold

• Infer modality dynamics goes beyond splicing events

  • Transcription rate of gene without intron or undergoing alternative splicing

  • Change rate of chromatin openess

  • More to Be Explored

• Serve as a plugin that can be seamlessly integrated into existing RNA velocity analysis pipelines

• Analyze dynamical systems in the context of multi-modal single cell data

Getting Started with GraphVelo

• Let’s get start with our quick_start_guide demo.

• Contribute to the project on github.

Installation

You need to have Python 3.8 or newer installed on your system.

To create and activate a new environment:

Install graphvelo via pip: