Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add TianGzlab/OmicsClaw --skill sc-cell-communicationgit clone --depth 1 https://github.com/TianGzlab/OmicsClawWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/tiangzlab/omicsclaw/sc-cell-communication)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/sc-cell-communication"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-cell-communication.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00069 | $0.02057 |
| Opus 5 | $0.00034 | $0.01028 |
| Sonnet 5 | $0.00014 | $0.00411 |
| Haiku 4.5 | $0.00007 | $0.00206 |
Grade A, and why
sc-cell-communication scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 3d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 154 lines — stays where its author put it; the contents beside it link to each section on GitHub.
sc-cell-communication
When to use
The user has an annotated scRNA AnnData (cell-type labels in
obs["cell_type"] or another column passed via --cell-type-key) and
wants ligand-receptor / sender-receiver interaction tables and figures.
Five backends:
builtin(default) — compact curated L-R set, heuristic score, no p-values.liana— Python LIANA rank aggregation (recommended general default).cellphonedb— official CellPhoneDB statistical workflow (human-only).cellchat_r— R-backed CellChat with pathway / centrality outputs.nichenet_r— R-backed NicheNet ligand prioritisation; needs explicit--receiver+--senders+--condition-*(human-only).
For TF → target gene regulatory networks use sc-grn. For cell-type
labelling use sc-cell-annotation.
Inputs & Outputs
Inputs
- Modalities: scrna
- File types:
.h5ad - Requires a preprocessed AnnData (
Xnormalised, PCA/neighbours present)
Outputs
tables/_matrix.csvtables/cellchat_centrality.csvtables/cellchat_count_matrix.csvtables/cellchat_pathways.csvtables/cellchat_results.csvtables/cellchat_weight_matrix.csvtables/cellphonedb_means.csvtables/cellphonedb_pvalues.csvtables/cellphonedb_significant_means.csvtables/group_role_summary.csvtables/lr_interactions.csvtables/meta.tsvtables/nichenet_ligand_activities.csvtables/nichenet_ligand_receptors.csvtables/nichenet_ligand_target_links.csvtables/nichenet_lr_network.csvtables/pathway_summary.csvtables/sender_receiver_summary.csvtables/top_interactions.csvfigures/r_ccc_bipartite.pngfigures/r_ccc_bubble.pngfigures/r_ccc_diff_network.pngfigures/r_ccc_heatmap.pngfigures/r_ccc_network.pngfigures/r_ccc_stat_bar.pngfigures/r_ccc_stat_scatter.pngfigures/r_ccc_stat_violin.pnginput.h5adprocessed.h5adreport.mdresult.json- Processed AnnData (
saves_h5ad)
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 3d ago First seen · 154 lines · 69 tokens per session scan A 3f351919ac19
sc-cell-communication is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 69 tokens to every session and 2,057 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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