muon-multiomics-singlecell

What problem does it solve?

This Skill streamlines the complex process of analyzing multi-modal single-cell data, such as combining RNA and ATAC-seq or RNA and protein expression from the same cells, enabling deeper biological insights.

Core Features & Use Cases

• Integrated Data Handling: Manages multiple data modalities (RNA, ATAC, protein, etc.) within a single MuData object.
• Joint Analysis: Performs dimensionality reduction (WNN graph) and clustering that integrates signals across modalities.
• Modality-Specific Preprocessing: Offers tailored preprocessing steps for different data types (e.g., TF-IDF for ATAC, CLR for proteins).
• Use Case: Analyze 10x Multiome data to identify cell types based on both gene expression and chromatin accessibility simultaneously, revealing cell states that might be missed by analyzing each modality alone.

Quick Start

Process a 10x Multiome dataset by running the full WNN clustering pipeline.