bio-splicing-quantification
Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative splice sites, mutually exclusive exons, and retained introns. Use when measuring splice site usage or isoform ratios from RNA-seq data.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-splicing-quantification --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: kallisto 0.50+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Splicing Quantification Quantify alternative splicing events as PSI (percent spliced in) values from RNA-seq data. ## Event Types | Type | Code | Description | |------|------|-------------| | Skipped exon | SE | Exon inclusion/exclusion | | Alternative 5' splice site | A5SS | Alternative donor site | | Alternative 3' splice site | A3SS | Alternative acceptor site | | Mutually exclusive exons | MXE | One of two exons included | | Retained intron | RI | Intron retention | ## Tool Selection ### SUPPA2 (transcript TPM-based) - Input: Transcript TPM from Salmon/kallisto - Faster, requires transcript quantification - Better for isoform-level analysis ### rMATS-turbo (BAM-based) - Input: Aligned BAM files - Junction read count
- Version Compatibility
- Event Types
- Tool Selection
- SUPPA2 (transcript TPM-based)
- rMATS-turbo (BAM-based)
- SUPPA2 Workflow
- rMATS-turbo Workflow
- Quality Thresholds
- Output Interpretation
- Related Skills
rMATS-turbo for BAM-based quantification rmats.py \
What does the bio-splicing-quantification skill do?
Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative splice sites, mutually exclusive exons, and retained introns. Use when measuring splice site usage or isoform ratios from RNA-seq data.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-splicing-quantification --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.