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 majiayu000/claude-skill-registry --skill 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.
# Neoantigen Prediction ## pVACtools Pipeline ```bash # Install pVACtools pip install pvactools # Or use conda for dependencies conda create -n pvactools python=3.8 conda activate pvactools pip install pvactools # Download IEDB tools pvactools download_iedb_tools ``` ## pVACseq Workflow ```bash # Run pVACseq on annotated VCF pvacseq run \ annotated.vcf \ sample_name \ "HLA-A*02:01,HLA-A*24:02,HLA-B*07:02,HLA-B*44:02" \ MHCflurry MHCnuggetsI \ output_dir \ -e1 8,9,10,11 \ --iedb-install-directory /path/to/iedb # Key parameters: # -e1: Epitope lengths for MHC-I (8-11) # -e2: Epitope lengths for MHC-II (15) # --binding-threshold: IC50 cutoff (default 500) # --percentile-threshold: Alternative cutoff ``` ## VCF Annotation Requirements ```bash # pVACseq requires VEP-annotated VCF # Must include transcript and amino acid changes # Run VEP first vep -i somatic.vcf -o annotated.vcf \ --cache --offline \ --format vcf --vcf \ --plugin Downstream \ --plugin Wildtype \ --terms SO \ --symbol ``` ## Parse pVACseq Results ```python import pandas as pd def parse_pvacseq_results(results_file): '''Parse pVACseq output Key columns: - Mutation: Gene and amino acid change - HLA Allele: Patient HLA pres
- pVACtools Pipeline
- pVACseq Workflow
- VCF Annotation Requirements
- Parse pVACseq Results
- Prioritize Neoantigens
- Alternative: Manual Neoantigen Pipeline
- Neoantigen Quality Metrics
- 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 majiayu000/claude-skill-registry --skill 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 majiayu000/claude-skill-registry, a repository with 534 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.