WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Performs over-representation analysis and GSEA for 30+ species.
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
Ancestry decomposition PCA against the Simons Genome Diversity Project
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.
Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safety profiles, and STITCH chemical-protein interactions. Performs predictive toxicology (AMES, DILI, LD50, carcinogenicity), organ/system toxicity profiling, chemical-gene-disease relationship mapping, regulatory safety extraction, and environmental hazard assessment. Use when asked about chemical toxicity, drug safety profiling, ADMET properties, environmental health risks, chemical hazard assessment, or toxicogenomic analysis.
AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks clinical trials from ClinicalTrials.gov using multi-dimensional matching across molecular eligibility, clinical criteria, drug-biomarker alignment, evidence strength, and geographic feasibility. Produces a quantitative Trial Match Score (0-100) per trial with tiered recommendations and a comprehensive markdown report. Use when oncologists, molecular tumor boards, or patients ask about clinical trial options for specific cancer types, biomarker profiles, or post-progression scenarios.
Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, transporters, pharmacodynamic), severity classification, clinical evidence grading, and provides management strategies. Supports single drug pairs, polypharmacy analysis (3+ drugs), and alternative drug recommendations. Use when users ask about drug interactions, medication safety, polypharmacy risks, or need DDI assessment for clinical decision support.
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.
Enforces explicit user permission before any file deletion. Activates when you're about to use rm, unlink, fs.rm, or any operation that removes files from disk. MUST be followed for all delete operations.
Ask users questions via the UI. Use when you need clarification, user preferences, or confirmation before proceeding. The user CANNOT see CLI output - this tool is the ONLY way to communicate with them.
Debug MLX ports by comparing against a PyTorch/diffusers reference via exported tensors/images (export-then-compare).
Three.js geometry creation - built-in shapes, BufferGeometry, custom geometry, instancing. Use when creating 3D shapes, working with vertices, building custom meshes, or optimizing with instanced rendering.
Three.js animation - keyframe animation, skeletal animation, morph targets, animation mixing. Use when animating objects, playing GLTF animations, creating procedural motion, or blending animations.
Three.js post-processing - EffectComposer, bloom, DOF, screen effects. Use when adding visual effects, color grading, blur, glow, or creating custom screen-space shaders.
Three.js interaction - raycasting, controls, mouse/touch input, object selection. Use when handling user input, implementing click detection, adding camera controls, or creating interactive 3D experiences.
Three.js materials - PBR, basic, phong, shader materials, material properties. Use when styling meshes, working with textures, creating custom shaders, or optimizing material performance.
Three.js shaders - GLSL, ShaderMaterial, uniforms, custom effects. Use when creating custom visual effects, modifying vertices, writing fragment shaders, or extending built-in materials.
