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bio-single-cell-cell-communication
Maintainer FreedomIntelligence · Last updated April 1, 2026
Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. Use when inferring ligand-receptor interactions between cell types.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-cell-communication
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- R: CellChat::createCellChat() → computeCommunProb() → netAnalysis().
- Python: liana.method.cellchat() (LIANA framework).
- Infer cell-cell communication from my scRNA-seq data" → Predict ligand-receptor interactions between cell types and visualize intercellular signaling networks. R: CellChat::createCellChat() → computeCommunProb() → netAnalysis() Python: liana.method.cellchat() (LIANA framework).
- cellchat <- createCellChat(object = seurat_obj, group.by = 'cell_type').
Source Doc
Excerpt From SKILL.md
CellChat (R)
Goal: Infer and quantify intercellular communication networks from scRNA-seq data using curated ligand-receptor databases.
Approach: Create a CellChat object from a Seurat object with cell type labels, select a signaling database subset, identify overexpressed ligands/receptors, compute communication probabilities using the trimean method, then aggregate into pathway-level networks.
library(CellChat)
library(Seurat)
## Set ligand-receptor database
CellChatDB <- CellChatDB.human # or CellChatDB.mouse
cellchat@DB <- CellChatDB
## Subset to secreted signaling (optional)
CellChatDB.use <- subsetDB(CellChatDB, search = 'Secreted Signaling')
cellchat@DB <- CellChatDB.use
Use cases
- Use when inferring ligand-receptor interactions between cell types.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- single-cell/clustering - Define cell types first
- single-cell/trajectory-inference - Communication along trajectory
- spatial-transcriptomics/spatial-communication - Spatial context
- pathway-analysis/go-enrichment - Pathway enrichment of targets
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