AG
Data & Repro
agent-browser
Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…
FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-ribo-seq-translation-efficiency
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-ribo-seq-translation-efficiency
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- R: riborex for differential TE with DESeq2 backend.
- Python: Ribo-seq/RNA-seq count ratio with statistical testing.
- Calculate translation efficiency from my Ribo-seq and RNA-seq" → Compute the ratio of ribosome occupancy to mRNA abundance per gene to identify translational regulation independent of transcription changes. R: riborex for differential TE with DESeq2 backend Python: Ribo-seq/RNA-seq count ratio with statistical testing.
- ribo_counts <- read.csv('ribo_counts.csv', row.names = 1) rna_counts <- read.csv('rna_counts.csv', row.names = 1).
Source Doc
Excerpt From SKILL.md
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 )
Use cases
- Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- rna-quantification - Get RNA-seq counts
- differential-expression - Compare expression
- orf-detection - Identify translated ORFs
Related skills
Related skills
AL
Data & Repro
alpha-vantage
Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators.
K-Dense-AI/claude-scientific-skillsView
BI
Data & Repro
bio-alignment-filtering
Filter alignments by flag, quality, region, or paired status.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-alignment-indexing
Index BAM/CRAM files with samtools index for random access.
FreedomIntelligence/OpenClaw-Medical-SkillsView