Skill Claude CodeCodex
Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building systems that actually work for neurodivergent minds.
Skill Claude CodeCodex
Manages allergy profiles including food, environmental, and drug allergies. Tracks reactions, identifies cross-reactivity risks, provides seasonal allergy forecasts, and warns about allergen exposure. Use when the user reports allergies, asks about cross-reactions, or needs allergen avoidance guidance.
Skill Claude CodeCodex
Orchestrates comprehensive annual checkup interpretation by coordinating report parsing, lab interpretation, family history analysis, genetic risk scoring, TCM constitution assessment, and guideline lookup. Use when the user uploads a checkup report or asks for help interpreting physical examination results.
Skill Claude CodeCodex
Parse Apple Health export (export.xml) and correlate wearable data with medical treatment history — optimized for oncology patients tracking health metrics across treatment cycles. Tracks heart rate, blood pressure, SpO2, weight, daily steps, and sleep, then overlays these onto treatment periods to reveal patterns.…
Skill Claude CodeCodex
Skill "autonomous-oncology-agent" from vitaclaw/vitaclaw, covering copyright notice, copyright (c) 2026 md babu mia, phd, all rights reserved, this code is proprietary and confidential and provenance: authenticated by md babu mia.
Skill Claude CodeCodex
Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.
Skill Claude CodeCodex
Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.
Skill Claude CodeCodex
Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a variant is common in the general population.
Skill Claude CodeCodex
Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
Skill Claude CodeCodex
Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.
Skill Claude CodeCodex
Query PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. Use when predicting drug response from genetic variants or implementing clinical pharmacogenomics.
Skill Claude CodeCodex
Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.
Skill Claude CodeCodex
Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.
Skill Claude CodeCodex
Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.
Skill Claude CodeCodex
Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.
Skill Claude CodeCodex
Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor mutations from plasma DNA or tracking specific variants.
Skill Claude CodeCodex
Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens. Use when designing vaccines, mapping antibody binding sites, or predicting immunogenic peptides.
Skill Claude CodeCodex
Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design. Use when prioritizing epitopes for vaccine development or identifying the most immunogenic neoantigens.
Skill Claude CodeCodex
Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences. Use when predicting MHC binding for vaccine design or neoantigen identification.
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
Skill "bio-liquid-biopsy-pipeline" from vitaclaw/vitaclaw, covering copyright notice, copyright (c) 2026 md babu mia, phd, all rights reserved, this code is proprietary and confidential and provenance: authenticated by md babu mia.
Skill Claude CodeCodex
Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction trends, mutation clearance kinetics, and defines molecular response criteria. Use when monitoring patients during therapy or detecting molecular relapse before clinical progression.
Skill Claude CodeCodex
Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific methylation signatures and performs tissue-of-origin deconvolution. Use when using methylation biomarkers for early cancer detection or minimal residual disease.
Skill Claude CodeCodex
Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations via HMM segmentation and calculates ctDNA percentage. Requires 0.1-1x sWGS coverage. Use when quantifying tumor burden from liquid biopsy or monitoring treatment response.