sc-cell-communication

name	sc-cell-communication
description	Cell-cell communication analysis for annotated scRNA-seq data using a built-in ligand-receptor scorer, LIANA, CellPhoneDB, CellChat, or a NicheNet R path.
version	0.3.0
author	OmicsClaw Team
license	MIT
tags	["singlecell","communication","ligand-receptor","liana","cellphonedb","cellchat","nichenet"]
metadata	{"omicsclaw":{"domain":"singlecell","allowed_extra_flags":["--cell-type-key","--cellchat-min-cells","--cellchat-prob-type","--cellphonedb-counts-data","--cellphonedb-iterations","--cellphonedb-pvalue","--cellphonedb-threshold","--cellphonedb-threads","--condition-key","--condition-oi","--condition-ref","--method","--nichenet-lfc-cutoff","--nichenet-expression-pct","--nichenet-top-ligands","--receiver","--senders","--species","--r-enhanced"],"param_hints":{"builtin":"[Truncated]","liana":"[Truncated]","cellphonedb":"[Truncated]","cellchat_r":"[Truncated]","nichenet_r":"[Truncated]"},"saves_h5ad":true,"requires_preprocessed":true,"requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"emoji":"S","homepage":"https://github.com/OmicsClaw/OmicsClaw","os":["macos","linux"],"install":["[Truncated]"],"trigger_keywords":["cell communication","cell-cell communication","ligand receptor","cellchat","liana","cellphonedb","nichenet"]}}

Single-Cell Cell Communication

Why This Exists

• Without it: ligand-receptor analysis is hard to standardize across tools.
• With it: the same cell-type labels can be reused across built-in and external communication backends.
• Why OmicsClaw: one output contract captures interactions, top pairs, and summary figures.

Core Capabilities

1. Five communication backends: built-in scorer, LIANA, CellPhoneDB, CellChat, and NicheNet.
2. Shared grouping contract: one cell_type_key-centric interface across all backends.
3. Method-correct matrix handling: LIANA / CellPhoneDB / CellChat use normalized expression, while NicheNet uses raw count-like input for receiver-vs-condition modeling.
4. Standard gallery: sender-receiver heatmap, bubble summary, role summary, pathway summary, plus NicheNet ligand ranking.
5. Downstream-ready export: annotated processed.h5ad, report, structured result JSON, README, tables/, figure_data/, and reproducibility bundle.

Scope Boundary

Implemented entry paths:

1. builtin
2. liana
3. cellphonedb
4. cellchat_r
5. nichenet_r

The wrapper assumes you already have biologically meaningful labels in obs.

Input Formats

Format	Extension / form	Current wrapper support	Notes
AnnData	.h5ad	yes	current direct input path
Demo	--demo	yes	bundled annotated-example fallback

Input Expectations

• Required column: a label column such as cell_type, leiden, or another supplied --cell-type-key.
• The grouping column should reflect biologically interpretable labels, not raw QC groups.
• Communication methods expect annotation or clustering to have already been resolved.

Workflow

1. Validate the grouping column and communication-specific prerequisites.