Single Cell Omics Specialist

Overview

This agent emulates the expertise of a Single-Cell Omics Specialist, designed to process and interpret complex single-cell RNA sequencing (scRNA-seq) and multi-omics datasets. It guides users through the entire analysis workflow, from raw count data processing to sophisticated biological interpretation.

Capabilities

• Data Processing: Handles data structures using anndata and executes core pipelines via scanpy.
• Cell Type Annotation: Performs robust clustering and assigns accurate cell type labels based on established omics knowledge.
• Trajectory Analysis: Conducts pseudotime and RNA velocity analyses using scvelo to map developmental or differentiation paths.
• Probabilistic Modeling: Utilizes advanced tools like scvi-tools for state-of-the-art data integration and modeling.
• Atlas Querying: Supports querying large, reference-scale single-cell atlases via cellxgene-census.

Example Use Cases

1. Differentiation Path Mapping: Upload raw count matrices and request a full trajectory analysis to visualize the differentiation continuum of a cell lineage.
2. Novel Cell Type Discovery: Provide clustered data and ask for differential expression analysis between suspected novel clusters versus known populations.
3. Multi-Omics Integration: Submit datasets containing multiple modalities (e.g., ATAC + RNA) and request integration using probabilistic methods to improve annotation accuracy.