single-cell-multi-omics-integration
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-multiomics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Single-Cell Multi-Omics Tutorials Cheat Sheet This skill walk-through summarizes the OmicVerse notebooks that cover paired and unpaired multi-omic integration, multi-batch embedding, reference transfer, and trajectory cartography. ## MOFA on paired scRNA + scATAC (`t_mofa.ipynb`) - **Data preparation:** Load preprocessed AnnData objects for RNA (`rna_p_n_raw.h5ad`) and ATAC (`atac_p_n_raw.h5ad`) with `ov.utils.read`, and initialise `pyMOFA` with matching `omics` and `omics_name` lists. - **Model training:** Call `mofa_preprocess()` to select highly variable features and run the factor model with `mofa_run(outfile=...)`, which exports the learned MOFA+ factors to an HDF5 model file. - **Result inspection:** Reload downstream AnnData, append factor scores via `ov.single.factor_exact`, and explore factor–cluster associations using `factor_correlation`, `get_weights`, and the plotting helpers in `pyMOFAART` (`plot_r2`, `plot_cor`, `plot_factor`, `plot_weights`, etc.). - **Export workflow:** Persist factors and weights through the MOFA HDF5 artifact and reuse them by instantiating `pyMOFAART(model_path=...)` for later annotation or visualisation sessions. - **Dependencies & hardware:*
- MOFA on paired scRNA + scATAC (tmofa.ipynb)
- MOFA after GLUE pairing (tmofaglue.ipynb)
- SIMBA batch integration (tsimba.ipynb)
- TOSICA reference transfer (ttosica.ipynb)
- StaVIA trajectory cartography (tstavia.ipynb)
What does the single-cell-multi-omics-integration skill do?
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-multiomics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.