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python-multimodal-10x

Run end-to-end multimodal single-cell RNA+ATAC analysis with Python tools.

1|Updated Nov 20, 2025
Search Tags:#python#multimodal#single-cell#atac#rna#muon#mudata
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill python-multimodal-10x
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: python-multimodal-10x
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/python-multimodal-10x
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill python-multimodal-10x

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

End-to-end multimodal single-cell analysis for RNA and ATAC data using Python tools (MuData/muon, Scanpy, SnapATAC2) to streamline integrated workflows on 10x Multiome and CITE-seq datasets.

Core Features & Use Cases

  • Integrated workflow: end-to-end RNA+ATAC processing, visualization, and cross-modality analysis.
  • ATAC preprocessing & integration: TF-IDF/LSI, Harmony batch correction, differential accessibility analyses.
  • Cross-platform compatibility: guidance for bridging to Seurat workflows and data exchanges between MuData and AnnData.

Quick Start

Install the required Python packages and run a minimal example to validate the multimodal pipeline.

Frequently Asked Questions about python-multimodal-10x

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run multimodal single-cell analysis for RNA and ATAC data in Python?▼

Run multimodal single-cell analysis by applying TF-IDF/LSI ATAC preprocessing, Harmony batch correction, and joint RNA+ATAC visualization using MuData, muon, scanpy, and SnapATAC2 for integrated 10x Multiome workflows.

What is the best way to integrate RNA and ATAC modalities for 10x Multiome datasets?▼

The best way to integrate RNA and ATAC modalities is using the muon and MuData framework to structure objects, applying Harmony for batch correction, and performing cross-modality visualizations with scanpy and SnapATAC2.

Do I need to install muon and mudata separately to process multimodal single-cell data?▼

Yes, you need to install core packages like muon, mudata, scanpy, snapatac2, episcanpy, scvi-tools, and harmonypy to run the multimodal single-cell pipeline, with optional tools available for extended functionality.

Can I use SnapATAC2 for differential accessibility analysis after RNA+ATAC preprocessing?▼

Yes, SnapATAC2 supports the workflow by applying TF-IDF/LSI ATAC preprocessing first, followed by differential accessibility analyses and joint RNA+ATAC visualization across modalities.

Does this Python multimodal workflow support data exchange with Seurat?▼

Yes, the workflow provides cross-platform compatibility guidance for bridging to Seurat workflows and facilitates data exchanges between MuData and AnnData structures for multimodal single-cell analysis.

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