Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via docking. Use when facing novel pathogens, emerging infections, or needing rapid therapeutic options during outbreaks.
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pharmacogenomic risk variants. Use when asked about drug safety, adverse events, post-market surveillance, or risk-benefit assessment.
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinical trials. Use when oncologist asks about treatment options for specific mutations (EGFR, KRAS, BRAF, etc.), therapy resistance, or clinical trial eligibility.
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, prioritizes genes for testing, interprets variants of uncertain significance. Use when clinician asks about rare disease diagnosis, unexplained phenotypes, or genetic testing interpretation.
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Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instruments, or running sensitivity analyses for causal inference.
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery. Use when identifying differentially abundant metabolites or building classification models.
Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities for causal variants, links variants to genes via L2G predictions, annotates functional consequences, and suggests validation strategies. Use when asked to fine-map GWAS loci, prioritize causal variants, identify credible sets, or link GWAS signals to causal genes.
Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.
Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve metabolomics study information from MetaboLights (MTBLS*) or Metabolomics Workbench (ST*), search for studies by keywords or disease, or generate comprehensive metabolomics research reports.
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels). Performs pathway enrichment, protein-pathway mapping, keyword searches, and systems-level analysis. Use when analyzing gene sets, exploring biological pathways, or investigating systems-level biology.
Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Given a disease/condition, genomic data (germline variants, somatic mutations, expression), and optional clinical parameters, performs multi-phase analysis across 9 phases covering disease disambiguation, genetic risk assessment, disease-specific molecular stratification, pharmacogenomic profiling, comorbidity/DDI risk, pathway analysis, clinical evidence and guideline mapping, clinical trial matching, and integrated outcome prediction. Generates a quantitative Precision Medicine Risk Score (0-100) with risk tier assignment (Low/Intermediate/High/Very High), treatment algorithm (1st/2nd/3rd line), pharmacogenomic guidance, clinical trial matches, and monitoring plan. Use when clinicians ask about patient risk stratification, treatment selection, prognosis prediction, or personalized therapeutic strategy across cancer, metabolic, cardiovascular, neurological, or rare diseases.
Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes between experimental groups.
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.
Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when testing whether an exposure causally affects an outcome using genetic instruments.
Analyze ab test analyzer operations. Auto-activating skill for Data Analytics. Triggers on: ab test analyzer, ab test analyzer Part of the Data Analytics skill category. Use when writing or running tests. Trigger with phrases like "ab test analyzer", "ab analyzer", "analyze ab test r".
Analyze response time analyzer operations. Auto-activating skill for Performance Testing. Triggers on: response time analyzer, response time analyzer Part of the Performance Testing skill category. Use when analyzing or auditing response time analyzer. Trigger with phrases like "response time analyzer", "response analyzer", "analyze response time r".
Analyze coverage report analyzer operations. Auto-activating skill for Test Automation. Triggers on: coverage report analyzer, coverage report analyzer Part of the Test Automation skill category. Use when analyzing or auditing coverage report analyzer. Trigger with phrases like "coverage report analyzer", "coverage analyzer", "analyze coverage report r".
Implement machine learning experiment tracking using MLflow or Weights & Biases. Configures environment and provides code for logging parameters, metrics, and artifacts. Use when asked to "setup experiment tracking" or "initialize MLflow". Trigger with relevant phrases based on skill purpose.
Set up Juicebox monitoring. Trigger: "juicebox monitoring", "juicebox metrics".
Execute iam policy reviewer operations. Auto-activating skill for Security Advanced. Triggers on: iam policy reviewer, iam policy reviewer Part of the Security Advanced skill category. Use when working with iam policy reviewer functionality. Trigger with phrases like "iam policy reviewer", "iam reviewer", "iam".
