AI-powered homologous recombination deficiency (HRD) analysis for PARP inhibitor response prediction using genomic scarring signatures and BRCA pathway assessment.
AI-powered circulating tumor DNA dynamics analysis for molecular residual disease detection, treatment response monitoring, and early relapse prediction using liquid biopsy.
AI-powered design of targeted gene panels for clinical and research applications including cancer diagnostics, pharmacogenomics, and rare disease testing.
AI-powered analysis of chromosomal instability (CIN) signatures for cancer prognosis, immunotherapy response prediction, and therapeutic vulnerability identification.
AI-powered analysis of coagulation disorders, thrombosis risk prediction, anticoagulation management, and platelet function assessment using machine learning.
AI-powered cell-free RNA analysis from liquid biopsy for cancer detection, tissue-of-origin identification, and non-invasive transcriptomic profiling.
AI-powered clonal hematopoiesis of indeterminate potential (CHIP) detection, risk stratification, and cardiovascular/malignancy risk prediction using genomic and clinical data.
AI-enhanced copy number variation calling and analysis from sequencing data for cancer genomics, constitutional CNV detection, and chromosomal aberration characterization.
AI-powered analysis of long-read sequencing data (PacBio, ONT) for structural variant detection, isoform discovery, epigenetic modifications, and de novo assembly.
AI-powered analysis of hemoglobin disorders including sickle cell disease, thalassemias, and variant hemoglobins using HPLC, electrophoresis, and molecular data.
AI-powered DNA methylation analysis using MethylGPT foundation models for epigenomic profiling, differential methylation detection, and cancer epigenome characterization.
Provides comprehensive tools for working with Electronic Health Records (EHR) using the HL7 FHIR standard.
AI-driven integration of cellular imaging, laser microdissection, and ultra-sensitive mass spectrometry for spatially-resolved single-cell proteomics.
AI-powered analysis of cellular senescence for aging research, cancer therapy response, and senolytic drug development.
AI-powered analysis of cancer metabolic reprogramming including Warburg effect, glutamine addiction, lipid metabolism, and metabolic vulnerabilities for therapeutic targeting.
AI-powered bone marrow morphology analysis, cell classification, and hematologic disorder diagnosis using deep learning on aspirate and biopsy images.
AI-powered comprehensive liquid biopsy analysis integrating ctDNA, CTCs, exosomes, and cfRNA for cancer detection, monitoring, and treatment guidance.
AI-guided CAR-T cell design for solid tumors using antigen prioritization, safety-by-design architectures, and exhaustion-resistant engineering.
AI-powered analysis for predicting optimal immune checkpoint inhibitor combinations based on tumor microenvironment, biomarkers, and molecular profiling.
AI-powered extracellular vesicle and exosome analysis for cancer biomarker discovery, liquid biopsy applications, and intercellular communication profiling.
AI-powered patient digital twin creation for clinical trial simulation, treatment outcome prediction, and personalized medicine using real-world data and multi-omics integration.
AI-powered integration of cryo-EM structural data with generative AI and molecular dynamics for structure-based drug design targeting flexible proteins and membrane complexes.
Perform spatial and temporal convergence analysis for solution verification — compute observed convergence orders from grid or timestep refinement studies, apply Richardson…
A multimodal precision oncology agent leveraging GPT-4 and vision transformers for cancer diagnosis, biomarker detection, and treatment planning.
Explore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection — generate Latin Hypercube, quasi-random, or factorial…
Handle mental health crisis situations in AI coaching safely. Use when implementing crisis detection, safety protocols, emergency escalation, or suicide prevention features.
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment.
Integrate multiple digital health data sources, connect to [WellAlly.tech](https://www.wellally.tech/) knowledge base, providing data import and knowledge reference for personal…
Map materials science terms, crystal structures, and sample descriptions to standardized ontology classes and properties — resolve natural-language concepts to ontology entries…
Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.). — from FreedomIntelligence/OpenClaw-Medical-Skills
Combines search results from multiple sources into coherent, deduplicated answers with source attribution.
Extract, analyze, and summarize simulation output data — pull spatial fields at specific timesteps, compute time-series trends and detect steady state, extract line profiles…
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates.
Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes — from…
Validate material sample annotations against ontology constraints — check that class names and property names exist in the ontology, verify domain and range consistency for object…
Detect crisis signals in user content using NLP, mental health sentiment analysis, and safe intervention protocols.
Select and configure nonlinear solvers for root-finding f(x)=0, optimization min F(x), and least-squares problems — choose among Newton, Newton-Krylov, quasi-Newton (BFGS,…
Query decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries into source-specific sy — from…
Generate correct, copy-pasteable SLURM sbatch job scripts and sanity-check HPC resource requests — configure nodes, MPI tasks, OpenMP threads, memory (per-node or per-cpu), GPUs,…
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visu — from…
Select and configure time integration methods for ODE and PDE simulations — choose among explicit Runge-Kutta, BDF, Rosenbrock, and Adams families, set relative and absolute error…
Select and apply numerical differentiation schemes for PDE and ODE discretization — generate finite-difference stencils at arbitrary order and accuracy, choose between central,…
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR.
Heart rate variability biometrics and emotional awareness training. Expert in HRV analysis, interoception training, biofeedback, and emotional intelligence.
Create publication-quality plots and visualizations using matplotlib and seaborn. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
Analyze numerical stability for time-dependent PDE simulations — check CFL and Fourier criteria, perform von Neumann stability analysis, detect stiffness, evaluate matrix…
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality sc — from…
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating mis — from…
Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.
Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building…
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography — from…
Validate simulations across three stages — run pre-flight checks on configuration files (parameter ranges, required fields, disk space), monitor runtime logs for residual growth,…
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructi — from…
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality contro — from…
Plan and control time-step policies for transient simulations — couple CFL and physics-based stability limits with adaptive stepping, ramp initial transients through sharp…
Plan and evaluate mesh generation for numerical simulations — estimate grid resolution from physics scales (interface width, boundary layers, wavelengths), check aspect ratios and…
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.