bio-ribo-seq-ribosome-stalling
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-ribo-seq-ribosome-stalling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+, numpy 1.26+, scipy 1.12+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Ribosome Stalling Detection **"Find ribosome pause sites in my data"** → Detect codon-level ribosome stalling and pausing events from Ribo-seq footprint density, identifying positions with abnormally high ribosome occupancy. - Python: `plastid` for codon-resolution density calculation, `scipy` for statistical scoring ## Concept Ribosome stalling/pausing occurs when ribosomes slow or stop at specific codons: - Rare codons (low tRNA availability) - Specific amino acid motifs (polyproline) - Regulatory pause sites (upstream of stress response genes) - Nascent chain interactions ## 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
- Version Compatibility
- Concept
- Calculate Codon-Level Occupancy
- Identify Pause Sites
- Codon-Specific Occupancy
- Correlate with Codon Usage
- Motif Analysis at Pause Sites
- Known Pause Motifs
- Related Skills
What does the bio-ribo-seq-ribosome-stalling skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-ribo-seq-ribosome-stalling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.