simo-multiomics-integration-agent - Spatial Multiomics Integration
Integrates spatial and single-cell multi-omics via probabilistic alignment
Tags
Updated: 2026-03-20Capabilities
Typical Inputs
Typical Outputs
What this skill does
- align scRNA-seq to spatial coordinates
- map chromatin accessibility spatially
- integrate methylation data spatially
- fuse multi-modal data layers
- assign cell types to spots
- identify spatial niches
- quantify mapping uncertainty
- smooth spatial predictions
- correct batch effects
Inputs
- spatial transcriptomics data
- single-cell RNA-seq reference
- single-cell ATAC-seq data
- single-cell methylation data
- CITE-seq protein data
- spatial modality reference
Outputs
- integrated spatial multi-omics object
- spatial cell type assignments
- spatial chromatin accessibility maps
- spatial niche assignments
- uncertainty maps
- gene activity scores
Requirements
- Python 3.10+
- Scanpy
- Squidpy
- Muon
- scvi-tools
- SnapATAC2
- Python Optimal Transport
- PyTorch
- GPyTorch