agentmods.dev

spatial-communication

spatial-communication is a skill for Claude Code, Codex from TianGzlab/OmicsClaw. It costs 82 tokens per session (1,813 once invoked), scanned A, original, Apache-2.0.

A workflow for estimating communication between labelled cell types in spatial transcriptomics using ligand-receptor pairs. Ligands are signalling molecules released by one cell, while receptors are molecules that can receive those signals on another cell.

In plain words
What is it for?
Use it to score ligand-receptor interactions, compare communication patterns, and export interaction, pathway, and cell-centrality tables.
Why use it?
It helps identify which cell-type pairs may be sending and receiving signals in tissue while taking their spatial dataset and labels into account.

Skill for Claude CodeCodex

not rated 160 1mo ago A scan 82 tokens original Apache-2.0
View the source file TianGzlab/OmicsClaw
Install

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.

agentmods
npx agentmods add skills/tiangzlab/omicsclaw/spatial-communication
Any agent
npx skills add TianGzlab/OmicsClaw --skill spatial-communication
Clone the repo
git clone --depth 1 https://github.com/TianGzlab/OmicsClaw

Made for: Claude Code, Codex.

Wrote 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.

agentmods badge for spatial-communication

README.md
[![agentmods](https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-communication.svg)](https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-communication)
Your own site
<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/spatial-communication"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/spatial-communication.svg" alt="Measured on agentmods" height="20"></a>
Per session 82 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,813 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5 $0.00082 $0.01813
Opus 5 $0.00041 $0.00907
Sonnet 5 $0.00016 $0.00363
Haiku 4.5 $0.00008 $0.00181

Measured yesterday against content hash dfe6345bc8c6, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

spatial-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 yesterday.

The scan reads SKILL.md. This mod also ships 2 executable files (spatial_communication.py, tests/test_spatial_communication.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

skills/spatial/spatial-communication/SKILL.md · 149 lines

How it starts

The opening of the file, as written. The whole thing — 149 lines — stays where its author put it; the contents beside it link to each section on GitHub.

spatial-communication

When to use

The user has a preprocessed spatial AnnData with cell-type labels (obs[cell_type_key], default leiden) and wants ligand-receptor cell-cell communication scored. Four backends:

  • liana (default) — LIANA consensus across multiple L-R methods. Tunables --liana-expr-prop, --liana-min-cells, --liana-n-perms.
  • cellphonedb — Permutation test with mean expression statistic. Tunables --cellphonedb-iterations, --cellphonedb-threshold.
  • fastccc — Fast permutation-free percentile-based score. Tunables --fastccc-min-percentile.
  • cellchat_r — CellChat (R) via rpy2 interop. Tunables --cellchat-min-cells, --cellchat-prob-type.

Species: --species human (default) or mouse. For non-spatial L-R use sc-cell-communication; for pathway scoring use spatial-enrichment.

Inputs & Outputs

Inputs

  • File types: .h5ad
  • Requires a preprocessed AnnData (X normalised, PCA/neighbours present)
  • Expects obsm: spatial

Outputs

  • tables/cellchat_centrality.csv
  • tables/cellchat_count_matrix.csv
  • tables/cellchat_pathways.csv
  • tables/cellchat_results.csv
  • tables/cellchat_weight_matrix.csv
  • tables/communication_run_summary.csv
  • tables/communication_spatial_points.csv
  • tables/communication_summary.csv
  • tables/communication_umap_points.csv
  • tables/complex_composition_table.csv
  • tables/complex_table.csv
  • tables/gene_table.csv
  • tables/interaction_table.csv
  • tables/lr_interactions.csv
  • tables/meta.tsv
  • tables/protein_table.csv
  • tables/signaling_roles.csv
  • tables/source_target_summary.csv
  • tables/top_interactions.csv
  • figures/communication_pvalue_distribution.png
  • figures/communication_roles_spatial.png
  • figures/communication_score_vs_significance.png
  • figures/lr_dotplot.png
  • figures/lr_heatmap.png
  • figures/lr_spatial.png
  • figures/signaling_roles.png
  • figures/source_target_summary.png
  • fastccc_input.h5ad
  • input.h5ad
  • processed.h5ad
  • report.md
  • result.json
  • Processed AnnData (saves_h5ad) — adds uns: ccc_results, liana_results, cellphonedb_results, fastccc_results, cellchat_results, communication_summary, communication_signaling_roles, spatial_communication

Read the full file on GitHub · 149 lines

Files

What ships with it

8 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.

Changes

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.

  1. yesterday First seen · 149 lines · 82 tokens per session scan A dfe6345bc8c6

Subscribe to this mod's changes

spatial-communication is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 82 tokens to every session and 1,813 once invoked, about $0.0004 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.

Scientificbioinformaticscellchatcellphonedbcommunicationfastcccknowledge-graphlianaligand-receptorllm-agentmulti-agentsmulti-omicsspatial
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