single-cell-multi-omics-integration
Installation
SKILL.md
Single-Cell Multi-Omics Integration
This skill covers OmicVerse's multi-omics integration tools for combining scRNA-seq, scATAC-seq, and other modalities. Each method addresses a different scenario—choose based on your data structure and analysis goal.
Method Selection Guide
Pick the right tool before writing any code:
| Scenario | Method | Key Class |
|---|---|---|
| Paired RNA + ATAC from same cells | MOFA directly | ov.single.pyMOFA |
| Unpaired RNA + ATAC (different experiments) | GLUE pairing → MOFA | ov.single.GLUE_pair → pyMOFA |
| Multi-batch single-modality integration | SIMBA | ov.single.pySIMBA |
| Transfer labels from annotated reference | TOSICA | ov.single.pyTOSICA |
| Trajectory on preprocessed multi-omic data | StaVIA | VIA.core.VIA |