Data & Analytics

Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions

Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

Ancestry decomposition PCA against the Simons Genome Diversity Project

Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling.

Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.

Complete 4-stage end-to-end research pipeline. Orchestrates idea-discovery-pipeline → deploy-experiment → auto-review-loop → generate-report. Reads RESEARCH_PLAN.md (or BRIEF.md as fallback) for context that overrides $ARGUMENTS.

Deploy and run experiments for ML/DL training (local, remote, or Modal GPU) AND spatial data science / GIScience experiments (local, data-driven). Reads from output/refine-logs/EXPERIMENT_PLAN.md and output/refine-logs/FINAL_PROPOSAL.md, writes to output/experiment/. Use when user says "run experiment", "deploy experiment", "execute experiment plan", or needs to launch training / spatial analysis jobs.

Precision editing tool that reduces abstract word count through intelligent compression techniques, maintaining scientific rigor while meeting strict journal and conference requirements.

Transform lengthy academic papers into concise, structured 250-word abstracts.

Designs internal, external, temporal, and functional validation strategies at the protocol stage for medical research studies.

Generates complete two-sample Mendelian randomization research designs from a user-provided outcome, exposure or exposure family, and robustness direction. Use when a study centers on summary-statistics causal inference with instrument selection, harmonization, IVW-primary estimation, complementary estimators, sensitivity analyses, optional multivariable upgrades, and conservative evidence interpretation. Covers five study patterns and always outputs Lite / Standard / Advanced / Publication+ ...

Generates complete tumor immune-infiltration-guided bulk-transcriptome diagnostic biomarker and machine-learning research designs from a user-provided cancer type and study direction. Always use this skill whenever a user wants to design, plan, or build a tumor bioinformatics study centered on differential expression, immune infiltration estimation, immune-linked module discovery, consensus feature selection, diagnostic modeling, nomogram construction, clinical association, and optional progn...

Designs studies for predicting treatment response or resistance in biomedical and clinical research. Always use this skill when the user needs a treatment-response or resistance prediction study blueprint rather than a prognostic biomarker protocol, diagnostic test design, causal treatment-effect estimation, or a completed manuscript. Focus on responder definition, treatment context, baseline comparability, feature integration strategy, model development logic, validation architecture, and in...

Designs a translational blueprint for moving a biomedical finding toward diagnosis, prognosis, treatment response prediction, patient stratification, or therapeutic development, with explicit translational milestones, validation thresholds, and feasibility-sensitive route framing.

Refines broad, vague, or aspirational biomedical research objectives into clear, bounded, measurable, executable, and downstream-ready study objective statements. Always use this skill when a user has a general aim such as “explore a mechanism,” “study prognosis,” “investigate biomarkers,” or “look at treatment response,” but the objective is still too broad, non-operational, or too ambiguous to support protocol framing, design selection, analysis planning, or hypothesis design. Never assume ...

Generates complete FAERS pharmacovigilance study designs for one-drug whole-profile safety mapping using signal detection, subgroup analysis, onset/seriousness characterization, and conservative label-gap interpretation.

Generates complete reference-grounded single-drug adverse-effect network-pharmacology research designs from a user-provided drug, adverse event, and desired evidence depth. Always use this skill when a user wants to design, plan, or upgrade a conventional network-pharmacology study centered on one fixed drug and one fixed adverse-effect endpoint, using drug-target prediction, adverse-event target collection, overlap analysis, PPI hub prioritization, enrichment interpretation, molecular dockin...

Generates complete reference-grounded single-drug adverse-effect network-pharmacology research designs from a user-provided drug, adverse event, and desired evidence depth. Always use this skill when a user wants to design, plan, or upgrade a conventional network-pharmacology study centered on one fixed drug and one fixed adverse-effect endpoint, using drug-target prediction, adverse-event target collection, overlap analysis, PPI hub prioritization, enrichment interpretation, molecular dockin...

Designs complete single-cell research plans from a user-provided biomedical direction. Always use this skill whenever a user wants to design, scope, or structure a single-cell study — including disease-focused, mechanism-focused, biomarker-focused, translational, perturbation-inspired, or validation-aware projects. It should define the research question, choose the best-fit study pattern, recommend sample grouping logic, suggest reference datasets as examples only, specify the core analysis m...

Plans sample size estimation logic, power assumptions, feasibility checks, and fallback enrollment strategies for clinical and translational study protocols.