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bio-ribo-seq-translation-efficiency
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-ribo-seq-translation-efficiency
- 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
- R：riborex ，用于 differential TE ，支持 DESeq2 backend。
- Python：Ribo-seq/RNA-seq count ratio ，支持 统计检验。
- Calculate translation efficiency ，面向 my Ribo-seq 、 RNA-seq" → Compute ratio of ribosome occupancy to mRNA abundance per gene to identify translational regulation independent of transcription changes. R：riborex ，用于 differential TE ，支持 DESeq2 backend Python：Ribo-seq/RNA-seq count ratio ，支持 统计检验。
- ribo_counts <- read.csv('ribo_counts.csv'，row.names = 1) rna_counts <- read.csv('rna_counts.csv'，row.names = 1)。
原始文档
SKILL.md 摘录
Concept
Translation Efficiency (TE) = Ribo-seq reads / RNA-seq reads
- TE > 1: Efficiently translated (more ribosomes per mRNA)
- TE < 1: Poorly translated
- Changes in TE indicate translational regulation
Sample information
sample_info <- data.frame( sample = colnames(ribo_counts), condition = factor(c('control', 'control', 'treated', 'treated')) )
Run riborex
results <- riborex( rnaCntTable = rna_counts, riboCntTable = ribo_counts, rnaCond = sample_info$condition, riboCond = sample_info$condition )
适用场景
- 适合在comparing translational regulation between conditions 或 identifying genes ，支持 altered translation independent of transcription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
- rna-quantification - Get RNA-seq counts
- differential-expression - Compare expression
- orf-detection - Identify translated ORFs
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