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 cell-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/cell-cell-communication)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/cell-cell-communication"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/cell-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 | $0.00009 | $0.02921 |
| Opus 5 | $0.00005 | $0.01460 |
| Sonnet 5 | $0.00002 | $0.00584 |
| Haiku 4.5 | $0.00001 | $0.00292 |
Grade A, and why
Cell-Cell Communication Analysis (CellChat) 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 7d 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 — 213 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Cell-Cell Communication Analysis (CellChat v2)
When to Use This Skill
✅ Use when:
- You have an annotated scRNA-seq dataset (Seurat object with cell type labels)
- You want to identify ligand-receptor interactions between cell types
- You want to visualize communication networks (chord diagrams, bubble plots)
- You want to find dominant sender/receiver cell populations
- Chains from
scrnaseq-seurat-core-analysisoutput (seurat_processed.rds)
❌ Don't use when:
- Data is not annotated (run
scrnaseq-seurat-core-analysisfirst) - You need spatial cell-cell communication (CellChat v2 supports this but requires spatial coordinates)
- You want gene regulatory networks (use
grn-pyscenicinstead) - You have bulk RNA-seq data
Installation
| Package | Version | License | Commercial Use | Installation |
|---|---|---|---|---|
| CellChat | ≥2.0.0 | GPL-3 | ✅ Permitted | devtools::install_github("jinworks/CellChat") |
| Seurat | ≥5.0.0 | MIT | ✅ Permitted | install.packages('Seurat') |
| SeuratData | ≥0.2.1 | GPL-3 | ✅ Permitted | devtools::install_github('satijalab/seurat-data') |
| NMF | ≥0.23.0 | GPL-2+ | ✅ Permitted | install.packages('NMF') |
| circlize | ≥0.4.12 | MIT | ✅ Permitted | install.packages('circlize') |
| ComplexHeatmap | ≥2.12.0 | MIT | ✅ Permitted | BiocManager::install('ComplexHeatmap') |
| ggprism | ≥1.0.3 | GPL-3 | ✅ Permitted | install.packages('ggprism') |
| presto | ≥1.0.0 | GPL-3 | ✅ Permitted | remotes::install_github('immunogenomics/presto') |
| ggalluvial | ≥0.12.0 | GPL-2 | ✅ Permitted | install.packages('ggalluvial') |
| rmarkdown | ≥2.20 | GPL-3 | ✅ Permitted | install.packages('rmarkdown') |
⚠️ CellChat must be installed from GitHub (not CRAN). Use the jinworks repository (active), not sqjin (archived).
Inputs
Required:
- Seurat object (.rds) with:
- Normalized expression data (
@assays$RNA@data) - Cell type annotations in metadata (e.g.,
celltypecolumn) - Minimum 3 cell types, ≥10 cells per type recommended
- Normalized expression data (
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.
- 7d ago First seen · 213 lines · 9 tokens per session scan A c0a2e3ec12bc
Cell-Cell Communication Analysis (CellChat) is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 9 tokens to every session and 2,921 once invoked, about $0.0000 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 2026-08-30.
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