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multimodal-anndata-mudata

Convert multi-assay Seurat objects to Python AnnData/MuData containers.

1|Updated Nov 20, 2025
Search Tags:#multimodal#anndata#seurat#multiomics#mudata#chromatin-assay#seurat-to-python
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill multimodal-anndata-mudata
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: multimodal-anndata-mudata
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/multimodal-anndata-mudata
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill multimodal-anndata-mudata

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Converts multi-assay R Seurat objects to Python AnnData/MuData and explains MuData container semantics for paired, unpaired, and partially paired multi-omics. Use when moving RNA+ATAC (or CITE-seq) data from Seurat/Signac into the scverse ecosystem, handling ChromatinAssay extraction, or setting up obs_names for the right pairing semantics. For R-only analysis see seurat-multimodal-analysis; for end-to-end Python analysis see python-multimodal-10x.

Core Features & Use Cases

  • Converts Seurat multimodal objects to MuData containers in Python (RNA+ATAC, CITE-seq, etc.)
  • Supports paired, unpaired, and partially paired data, with correct obs_names mapping
  • Requires or complements existing skills: anndatar-seurat-scanpy-conversion, python-multimodal-10x, seurat-multimodal-analysis

Quick Start

Export Seurat objects to AnnData-compatible formats and assemble a MuData container in Python to enable paired, unpaired, or partially paired multi-omics analysis.

Frequently Asked Questions about multimodal-anndata-mudata

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

FAQPage Schema
How do I convert a Seurat multimodal object to Python MuData?▼

To convert a Seurat multimodal object to Python MuData, export the multi-assay Seurat object to AnnData-compatible formats and assemble them into a MuData container, handling ChromatinAssay extraction and obs_names pairing semantics.

What is the best way to transfer RNA and ATAC data from Seurat to the scverse ecosystem?▼

The best way to transfer RNA and ATAC data from Seurat to the scverse ecosystem is converting the Seurat object into AnnData/MuData containers, which correctly maps paired, unpaired, or partially paired multi-omics obs_names.

Does MuData support paired, unpaired, and partially paired multi-omics data?▼

Yes, MuData supports paired, unpaired, and partially paired multi-omics data by using specific obs_names mapping semantics to align RNA, ATAC, or CITE-seq assays during the Seurat to Python conversion.

How does ChromatinAssay extraction work when moving Signac objects to Python?▼

ChromatinAssay extraction works by isolating the chromatin accessibility assay from the Seurat or Signac object during conversion, ensuring its specific data structure is preserved within the resulting Python AnnData or MuData container.

Do I need anndatar-seurat-scanpy-conversion skills before converting to MuData?▼

Yes, you need prerequisite skills like anndatar-seurat-scanpy-conversion, python-multimodal-10x, and seurat-multimodal-analysis to properly set up the environment and data formats before assembling the MuData container.

Why does obs_names pairing fail when converting Seurat CITE-seq data to AnnData?▼

obs_names pairing fails during Seurat CITE-seq conversion when the mapping semantics for paired, unpaired, or partially paired multi-omics assays are not correctly configured before assembling the MuData container.

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