single-cell-multi-omics-integration - Single-cell multi-omics integration
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
Tags
Updated: 2026-09-16Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Integrate paired RNA and ATAC
- Integrate unpaired data with GLUE
- Perform SIMBA batch integration
- Transfer annotations using TOSICA
- Map cell trajectories using StaVIA
Inputs
- Preprocessed AnnData RNA and ATAC objects
- GLUE-derived embeddings
- Reference AnnData and gene-set GMT files
- Single-cell velocity datasets
Outputs
- MOFA HDF5 factor model files
- Harmonized AnnData with SIMBA embeddings
- TOSICA project folder and checkpoints
- Pseudotime plots and GIF streamplot animations
Requirements
- mofapy2 package
- scglue and scvi-tools packages
- simba and simba_pbg packages
- PyTorch transformer environment
- scvelo and pyVIA packages