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Data & Repro
BI
bio-single-cell-multimodal-integration
Maintainer FreedomIntelligence · Last updated April 1, 2026
Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA + protein or RNA + ATAC. Use when analyzing CITE-seq, Multiome, or other multi-modal single-cell data.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-multimodal-integration
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- R: Seurat::FindMultiModalNeighbors() for WNN integration.
- Python: muon for MuData handling, scanpy + anndata for multimodal objects.
- Integrate RNA and protein data from my CITE-seq experiment" → Jointly analyze multiple modalities (RNA + protein, RNA + ATAC) measured in the same cells using weighted nearest neighbor or factor analysis. R: Seurat::FindMultiModalNeighbors() for WNN integration Python: muon for MuData handling, scanpy + anndata for multimodal objects.
- Analyze multi-modal single-cell data where multiple measurements are made per cell.
- data <- Read10X('filtered_feature_bc_matrix/').
Source Doc
Excerpt From SKILL.md
Common Modalities
| Technology | Modalities | Package |
|---|---|---|
| CITE-seq | RNA + surface proteins (ADT) | Seurat |
| 10X Multiome | RNA + ATAC | Seurat, Signac, ArchR |
| SHARE-seq | RNA + ATAC | Seurat, Signac |
| Spatial (Visium) | RNA + spatial coordinates | Seurat, Squidpy |
Separate RNA and ADT
rna_counts <- data$Gene Expression
adt_counts <- data$Antibody Capture
Create Seurat object with both assays
obj <- CreateSeuratObject(counts = rna_counts, assay = 'RNA') obj[['ADT']] <- CreateAssayObject(counts = adt_counts)
Use cases
- Use when working with data that measures multiple modalities per cell like RNA + protein or RNA + ATAC.
- Use when analyzing CITE-seq, Multiome, or other multi-modal single-cell data.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- single-cell/data-io - Loading single-cell data
- single-cell/clustering - Clustering methods
- single-cell/markers-annotation - Cell type annotation
- chip-seq/peak-calling - For ATAC peak calling
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