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bio-ribo-seq-ribosome-stalling
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon-specific translation dynamics.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-ribo-seq-ribosome-stalling
- 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
- Python：plastid ，用于 codon-resolution density calculation，scipy ，用于 statistical scoring。
- Find ribosome pause sites in my data" → Detect codon-level ribosome stalling 、 pausing events ，面向 Ribo-seq footprint density，identifying positions ，支持 abnormally high ribosome occupancy. Python：plastid ，用于 codon-resolution density calculation，scipy ，用于 statistical scoring。
- Rare codons (low tRNA availability)。
- Specific amino acid motifs (polyproline)。
- Regulatory pause sites (upstream of stress response genes)。
原始文档
SKILL.md 摘录
Calculate Codon-Level Occupancy
Goal: Quantify ribosome occupancy at each codon position across all transcripts.
Approach: Map reads to P-sites using a fixed offset, then bin counts into codons along each CDS.
Identify Pause Sites
Goal: Detect codon positions with significantly elevated ribosome occupancy indicative of translational pausing.
Approach: Z-score normalize occupancy per transcript and flag positions exceeding a threshold (default z > 3).
Codon-Specific Occupancy
Goal: Calculate average ribosome occupancy for each of the 64 codon types across all genes.
Approach: Aggregate read density per codon identity across all CDS positions and compute per-codon mean occupancy.
适用场景
- 适合在studying translational regulation，identifying pause sites，或 analyzing codon-specific translation dynamics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
- ribosome-periodicity - Validate data quality
- orf-detection - Context for pause sites
- translation-efficiency - Gene-level translation
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