AN
数据与复现
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observ…
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数据与复现
SI
simo-multiomics-integration-agent
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Single-cell multi-omics integration with SIMO/MOFA+ for joint embedding.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/simo-multiomics-integration-agent
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- SIMO Multiomics Integration Agent performs spatial integration of multi-omics 数据集s through probabilistic alignment. Unlike previous tools limited to transcriptomics，SIMO integrates spatial transcriptomics ，支持 single-cell RNA-seq 、 expands to chromatin accessibility，DNA methylation，、 proteomics data。
- When integrating spatial transcriptomics ，支持 single-cell multi-omics data。
- 用于 constructing comprehensive tissue atlases ，支持 spatial context。
- To map epigenomic states (ATAC-seq，methylation) onto spatial coordinates。
- When analyzing multi-modal cellular phenotypes in tissue architecture。
原始文档
SKILL.md 摘录
Core Capabilities
-
Spatial-scRNA Integration: Probabilistically align single-cell RNA-seq to spatial coordinates.
-
Chromatin Accessibility Mapping: Project scATAC-seq profiles onto spatial tissue locations.
-
DNA Methylation Spatial Mapping: Integrate single-cell methylation data with spatial context.
-
Multi-Modal Fusion: Combine transcriptomic, epigenomic, and proteomic layers.
-
Probabilistic Cell-Type Assignment: Assign cell types to spatial spots with uncertainty quantification.
-
Spatial Niche Identification: Discover cellular niches defined by multi-omic signatures.
Supported Modalities
| Modality | Input Format | Spatial Reference |
|---|---|---|
| scRNA-seq | AnnData, Seurat | Visium, MERFISH, Xenium |
| scATAC-seq | SnapATAC2, ArchR | Visium, Slide-seq |
| scMethyl | Bismark, allcools | Any spatial modality |
| CITE-seq (protein) | AnnData | Spatial proteomics |
| Multi-ome (RNA+ATAC) | Muon, SnapATAC2 | All platforms |
Integration Algorithm
| Step | Method | Purpose |
|---|---|---|
| Feature Selection | HVG + marker genes | Reduce dimensionality |
| Embedding | Variational autoencoder | Shared latent space |
| Alignment | Optimal transport | Probabilistic matching |
| Spatial Mapping | Gaussian processes | Smooth spatial predictions |
| Uncertainty | Posterior sampling | Confidence intervals |
适用场景
- When integrating spatial transcriptomics ，支持 single-cell multi-omics data。
- 用于 constructing comprehensive tissue atlases ，支持 spatial context。
- To map epigenomic states (ATAC-seq，methylation) onto spatial coordinates。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- scGPT_Agent - For foundation model embeddings
- Spatial_Epigenomics_Agent - For spatial epigenomics analysis
- Cell_Cell_Communication - For ligand-receptor analysis
- Nicheformer_Spatial_Agent - For spatial niche modeling
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