bio-immunoinformatics-neoantigen-prediction
Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient HLA and may elicit T-cell responses. Use when identifying vaccine targets or checkpoint inhibitor response biomarkers from tumor sequencing data.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-immunoinformatics-neoantigen-prediction --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: Ensembl VEP 111+, MHCflurry 2.1+, pVACtools 4.1+, 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. # Neoantigen Prediction **"Identify neoantigens from my tumor mutations"** → Predict mutant peptides from somatic variants that bind patient HLA alleles and may elicit T-cell responses for personalized cancer immunotherapy. - CLI: `pvacseq run` with VEP-annotated VCF and patient HLA types (pVACtools) ## pVACtools Pipeline (Ensembl VEP 111+) **Goal:** Install pVACtools and its IEDB prediction engine dependencies. **Approach:** Install via pip (optionally in a dedicated conda environment) and download IEDB tools for binding prediction. ```bash # Install pVACtools pip install pvactools # Or use conda for dependencies conda create -n pvactools python=3.8 conda activate pvactools pip install p
- Version Compatibility
- pVACtools Pipeline (Ensembl VEP 111+)
- pVACseq Workflow (Ensembl VEP 111+)
- VCF Annotation Requirements (Ensembl VEP 111+)
- Parse pVACseq Results
- Prioritize Neoantigens (Ensembl VEP 111+)
- Alternative: Manual Neoantigen Pipeline (Ensembl VEP 111+)
- Neoantigen Quality Metrics (Ensembl VEP 111+)
- Related Skills
Install pVACtools pip install pvactools Or use conda for dependencies conda create -n pvactools python=3.8 conda activate pvactools Download IEDB tools pvactools download_iedb_tools Run pVACseq on annotated VCF pvacseq run \ annotated.vcf \
What does the bio-immunoinformatics-neoantigen-prediction skill do?
Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient HLA and may elicit T-cell responses. Use when identifying vaccine targets or checkpoint inhibitor response biomarkers from tumor sequencing data.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-immunoinformatics-neoantigen-prediction --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.