single-cell-cellphonedb-communication-mapping
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cellphone-db --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 CellPhoneDB communication mapping ## Overview Apply this skill when a user wants to quantify ligand–receptor communication between annotated single-cell populations and display the networks with `CellChatViz`. It distils the workflow from [`t_cellphonedb.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_cellphonedb.ipynb), which analyses EVT trophoblast data. ## Instructions 1. **Prepare the environment** - Use an environment with `omicverse>=0.2`, `scanpy`, `anndata`, `pandas`, `matplotlib`, and `cellphonedb` resources. The tutorial assumes the pre-built CellPhoneDB v5 SQLite bundle downloaded as `cellphonedb.zip` in the working directory. - Activate omicverse plotting defaults via `ov.plot_set()` so that downstream figures follow the project palette. 2. **Load and subset the annotated AnnData object** - Read the normalised counts with `adata = ov.read('data/cpdb/normalised_log_counts.h5ad')`. - Filter to the cell populations of interest using `adata.obs['cell_labels']` (e.g., EVT, dNK, VCT). Ensure `adata.obs['cell_labels']` is categorical and free of missing values so CellPhoneDB groups cells correctly. - Confirm values are log-normalised (`adata.X.max()` shoul
- Overview
- Instructions
- Examples
- References
What does the single-cell-cellphonedb-communication-mapping skill do?
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-cellphone-db --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.