AR
Data & Repro
armored-cart-design-agent
Design armored CAR-T cells with cytokine payloads and resistance mechanisms.
FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-immunoinformatics-neoantigen-prediction
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-immunoinformatics-neoantigen-prediction
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: pvacseq run with VEP-annotated VCF and patient HLA types (pVACtools).
- 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).
- conda create -n pvactools python=3.8 conda activate pvactools pip install pvactools.
Source Doc
Excerpt From SKILL.md
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.
## Download IEDB tools
pvactools download_iedb_tools
pVACseq Workflow (Ensembl VEP 111+)
Goal: Run the full pVACseq neoantigen prediction pipeline on a VEP-annotated VCF.
Approach: Provide annotated VCF with patient HLA alleles and select binding prediction algorithms; pVACseq generates mutant peptides and predicts MHC binding.
Use cases
- Use when identifying vaccine targets or checkpoint inhibitor response biomarkers from tumor sequencing data.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- immunoinformatics/mhc-binding-prediction - MHC binding details
- immunoinformatics/immunogenicity-scoring - Prioritization
- variant-calling/variant-calling - Input somatic mutations
Related skills
Related skills
AR
Data & Repro
arxiv-search
Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.
FreedomIntelligence/OpenClaw-Medical-SkillsView
AU
Data & Repro
autonomous-oncology-agent
Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis generation.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-cfdna-preprocessing
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate remo…
FreedomIntelligence/OpenClaw-Medical-SkillsView