scgpt

What problem does it solve?

This Skill addresses the challenge of embedding and annotating single-cell expression data with scGPT, a foundation model for single-cell biology.

Core Features & Use Cases

• Cell Embedding: Generate cell embeddings from AnnData for clustering and integration.
• Cell-Type Annotation: Perform zero-shot or fine-tuned cell-type annotation.
• Gene-Level Representation: Obtain gene-level representations for perturbation and GRN tasks.
• Use Case: Ideal for researchers in single-cell biology who need to analyze and annotate large datasets to understand cellular processes.

Quick Start

Run the scgpt skill to produce cell embeddings from your AnnData file.