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bgpt-paper-search
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数据与复现
SI
single-cell-rna-qc
维护者 FreedomIntelligence · 最近更新 2026年4月1日
single-cell-rna-qc：执行 quality control on single-cell RNA-seq data (.h5ad 或.h5 files) ，使用 scverse best practices ，支持 MAD-based filtering 、 comprehensive visualizations。 适合在users request QC analysis，filtering low-quality cells，assessing data quality，或 following scverse/scanpy best practices ，用于 single-cell analysis时使用。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-cell-rna-qc
- 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
- Automated QC workflow ，用于 single-cell RNA-seq data following scverse best practices。
- Standard QC workflow ，支持 adjustable thresholds (all cells filtered same way)。
- Batch processing multiple 数据集s。
- Quick exploratory analysis。
- User wants "just works" solution。
原始文档
SKILL.md 摘录
When to Use This Skill
Use when users:
- Request quality control or QC on single-cell RNA-seq data
- Want to filter low-quality cells or assess data quality
- Need QC visualizations or metrics
- Ask to follow scverse/scanpy best practices
- Request MAD-based filtering or outlier detection
Supported input formats:
.h5adfiles (AnnData format from scanpy/Python workflows).h5files (10X Genomics Cell Ranger output)
Default recommendation: Use Approach 1 (complete pipeline) unless the user has specific custom requirements or explicitly requests non-standard filtering logic.
Approach 1: Complete QC Pipeline (Recommended for Standard Workflows)
For standard QC following scverse best practices, use the convenience script scripts/qc_analysis.py:
python3 scripts/qc_analysis.py input.h5ad
## Workflow Steps
The script performs the following steps:
1. **Calculate QC metrics** - Count depth, gene detection, mitochondrial/ribosomal/hemoglobin content
2. **Apply MAD-based filtering** - Permissive outlier detection using MAD thresholds for counts/genes/MT%
3. **Filter genes** - Remove genes detected in few cells
4. **Generate visualizations** - Comprehensive before/after plots with threshold overlays
适用场景
- Request quality control 或 QC on single-cell RNA-seq data。
- Want to filter low-quality cells 或 assess data quality。
- Need QC visuali。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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