spatial-communication

name	spatial-communication
description	Cell-cell communication analysis for spatial transcriptomics using LIANA, CellPhoneDB, FastCCC, or CellChat, with method-specific parameter hints and standardized ligand-receptor outputs.
version	0.5.0
author	OmicsClaw Team
license	MIT
tags	["spatial","communication","ligand-receptor","liana","cellphonedb","fastccc","cellchat"]
metadata	{"omicsclaw":{"domain":"spatial","allowed_extra_flags":["--cell-type-key","--method","--species","--liana-expr-prop","--liana-min-cells","--liana-n-perms","--liana-resource","--cellphonedb-iterations","--cellphonedb-threshold","--fastccc-single-unit-summary","--fastccc-complex-aggregation","--fastccc-lr-combination","--fastccc-min-percentile","--cellchat-prob-type","--cellchat-min-cells"],"param_hints":{"liana":"[Truncated]","cellphonedb":"[Truncated]","fastccc":"[Truncated]","cellchat_r":"[Truncated]"},"legacy_aliases":["communication"],"saves_h5ad":true,"requires_preprocessed":true,"requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"emoji":"📡","homepage":"https://github.com/TianGzlab/OmicsClaw","os":["macos","linux"],"install":["[Truncated]"],"trigger_keywords":["cell communication","cell-cell communication","ligand receptor","ligand-receptor","LIANA","CellPhoneDB","FastCCC","CellChat"]}}

📡 Spatial Communication

You are Spatial Communication, the OmicsClaw skill for ligand-receptor interaction analysis in spatial transcriptomics data. The skill exposes four backends with different statistical assumptions and now keeps their core parameters method-specific instead of flattening them into a generic interface.

Why This Exists

• Without it: users often mix up matrix assumptions, species support, and communication scores across LIANA, CellPhoneDB, FastCCC, and CellChat.
• With it: one command runs a method-correct communication workflow, exports a standardized LR table, and keeps a reproducible parameter record.
• Why OmicsClaw: the wrapper normalizes output structure while still preserving method-specific tuning hints, guardrails, and downstream UX.

Core Capabilities

1. LIANA: multi-method consensus communication ranking through liana.mt.rank_aggregate.
2. CellPhoneDB: official statistical permutation method with iterations and threshold controls.
3. FastCCC: permutation-free communication analysis through the public statistical_analysis_method API.
4. CellChat (R): R-based communication inference with pathway and centrality exports.
5. Standard Python gallery: emits a recipe-driven communication gallery with LR overviews, role diagnostics, supporting summaries, and uncertainty panels built on shared skills/spatial/_lib/viz primitives.
6. Standardized LR outputs: all methods are normalized to the same columns: ligand, receptor, source, target, score, pvalue.
7. Communication summaries: exports aggregated source-target communication summaries plus signaling-role classification.
8. Method-aware reproducibility: only the parameters relevant to the selected method are written to reproducibility/commands.sh.

Input Formats

Format	Extension	Required Fields	Example
AnnData (preprocessed)	.h5ad	X (log-normalized), , or another cell type column