skills.rest
tony-zhelonkin
tony-zhelonkinCOMMUNITY
Explore all skills by this author →
𝕏@TonyZhelonkinGitHub

seurat-multimodal-analysis

Consolidate multimodal single-cell RNA, protein, and chromatin data with Seurat and Signac.

1|Updated Nov 20, 2025
Search Tags:#multimodal#scRNA-seq#seurat#wnn#signac#chromvar
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill seurat-multimodal-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: seurat-multimodal-analysis
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/seurat-multimodal-analysis
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill seurat-multimodal-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill provides a comprehensive, end-to-end workflow for multimodal single-cell analysis in R using Seurat and Signac, enabling integrated interpretation of RNA, ADT, and ATAC data within a single consistent framework.

Core Features & Use Cases

  • Multi-assay object management (RNA, ADT, ATAC, peaks) and seamless integration across modalities.
  • Weighted Nearest Neighbors (WNN) analysis for joint embeddings and robust clustering of multimodal data.
  • CITE-seq processing (RNA + protein) and 10x Multiome workflows with chromatin accessibility analysis via Signac.
  • Gene activity scoring, motif analysis with ChromVAR, peak-gene linkage, and Azimuth bridge/reference mapping for cell type annotation.
  • Cross-modality integration for unpaired data and multi-sample integration workflows.

Quick Start

Load a Seurat object with RNA, ADT, and ATAC assays and run the included multimodal workflow to generate a WNN-based UMAP with basic cluster annotation.

Frequently Asked Questions about seurat-multimodal-analysis

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

FAQPage Schema
How do I integrate scRNA-seq and ATAC data using Seurat WNN?▼

Seurat WNN integrates scRNA-seq and ATAC data by constructing a joint multimodal neighborhood graph, enabling robust clustering and unified UMAP visualization across RNA and chromatin modalities.

Can I use Signac for chromatin accessibility and motif analysis in CITE-seq workflows?▼

Signac integrates with CITE-seq workflows to analyze chromatin accessibility, performing gene activity scoring, ChromVAR motif analysis, and peak-gene linkage alongside RNA and ADT modalities.

What is the best way to map cell types in multimodal single-cell data?▼

Azimuth bridge and reference mapping annotate cell types in multimodal single-cell data by transferring labels from curated references to integrated WNN embeddings across RNA, ADT, and ATAC assays.

Does Seurat support unpaired multi-sample integration for scRNA-seq and ATAC?▼

Seurat supports unpaired multi-sample integration for scRNA-seq and ATAC data, providing cross-modality integration workflows that standardize dimensionality reduction and clustering across disparate tissue samples.

How do I run a 10x Multiome analysis pipeline in R?▼

Run a 10x Multiome analysis pipeline in R using Seurat and Signac to perform QC, normalization, peak calling, and WNN integration for joint interpretation of RNA and chromatin accessibility.

When should I use WNN instead of standard integration for multimodal scRNA-seq?▼

Use WNN instead of standard integration for multimodal scRNA-seq when accurate cell type identification requires weighting RNA, protein, and chromatin modalities simultaneously to resolve closely related cellular states.

Related Skills

Explore More Data & Analytics Skills→
ya-wayya-way

bio-single-cell-multimodal-integration

Integrate multi-modal single-cell RNA, protein, and ATAC data into unified representations.

Community
Advanced
inflexa-aiinflexa-ai
29

enrichment

Run GSEA, ORA, and decoupler enrichment on gene expression data.

Official
Advanced
CHENyiru3CHENyiru3

signac

Integrate scATAC-seq chromatin accessibility analysis with Seurat workflows.

Community
Intermediate
jasrajtulsijasrajtulsi

scanpy

Process single-cell RNA-seq datasets into quality-controlled AnnData outputs with clustering and marker discovery.

Community
Advanced