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数据与复现单细胞与空间组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现
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bio-spatial-transcriptomics-spatial-preprocessing

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identify highly variable genes. Use when filtering and normalizing spatial transcriptomics data.

OpenClawNanoClaw分析处理复现实验bio-spatial-transcriptomics-spatial-preprocessing🧬 bioinformatics (gptomics bio-* suite)bioinformatics — single-cell & spatial omicsquality

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-spatial-transcriptomics-spatial-preprocessing

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

2 min

核心说明

  • Python：scanpy.pp.calculate_qc_metrics() → filter_cells() → normalize_total() on spatial AnnData。
  • Preprocess my spatial transcriptomics data" → Calculate spatial QC metrics (genes/spot，mitochondrial fraction)，filter spots by expression 、 tissue coverage，normalize，、 select variable genes. Python：scanpy.pp.calculate_qc_metrics() → filter_cells() → normalize_total() on spatial AnnData。
  • QC，filtering，normalization，、 feature selection ，用于 spatial data。
  • sc.pp.calculate_qc_metrics(adata，inplace=True)。

原始文档

SKILL.md 摘录

Calculate QC Metrics

Goal: Compute per-spot and per-gene quality control statistics.

Approach: Use Scanpy's calculate_qc_metrics to generate total counts, gene counts, and other summary statistics.


## View QC columns

print(adata.obs[['total_counts', 'n_genes_by_counts']].describe())
print(adata.var[['total_counts', 'n_cells_by_counts']].describe())

Calculate Mitochondrial Content

Goal: Quantify mitochondrial gene expression as a quality indicator.

Approach: Flag MT-prefixed genes, then compute percentage of counts from mitochondrial genes per spot.

适用场景

  • 适合在filtering 、 normalizing spatial transcriptomics data时使用。

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

  • spatial-data-io - Load spatial data
  • spatial-neighbors - Build spatial graphs
  • single-cell/preprocessing - Non-spatial preprocessing

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