Skill rating

Query InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, and 11 other member databases. Use for protein function prediction, do

Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifying questions

Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, Gl

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene di

Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretati

Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs). Search by TF name, species, or class; scan DNA sequences for TF binding sites; compare matrices; essential for regulator

You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.

Query GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative trait loci), and sQTLs. Essential for linking GWAS variants to gene regulation, under

Use when you have a spec or requirements for a multi-step task, before touching code

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding

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 vulnerabilit

Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extrac

Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, and optional biomarkers (TMB, PD-L1, MSI status), performs sy

Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Given a disease/condition, genomic data (germline variants, somatic mutations, expre

Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and optional cancer type, performs multi-database analysis co

Comprehensive structural variant (SV) analysis skill for clinical genomics. Classifies SVs (deletions, duplications, inversions, translocations), assesses pathogenicity using ACMG-adapted criteria, ev

Comprehensive computational validation of drug targets for early-stage drug discovery. Evaluates targets across 10 dimensions (disambiguation, disease association, druggability, chemical matter, clini

Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease context from spatial transcriptom

Systematic clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Aggregates evidence from ClinVar, gnomAD, CIViC, UniProt, and PDB

Strategic clinical trial design feasibility assessment using ToolUniverse. Evaluates patient population sizing, biomarker prevalence, endpoint selection, comparator analysis, safety monitoring, and re

Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, transporters, pharmacodynamic), severity classification, clinical evidence grading, a

Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinica

Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safety profiles, and STITCH chemical-protein interactions.

Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation st

Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-lev

Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. Use when analyzing genomics data, searching

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, qual

Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding r

Use when you have a written implementation plan to execute in a separate session with review checkpoints

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial g

Presentation creation, editing, and analysis. When Claude needs to work with presentations (.pptx files) for: (1) Creating new presentations, (2) Modifying or editing content, (3) Working with layouts

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web search for accurate data. Supports 1

Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing

Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this

RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome d

Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3 characteristics, convergence

Conduct comprehensive literature research with target disambiguation, evidence grading, and structured theme extraction. Creates a detailed report with mandatory completeness checklist, biological mod

Integrate and analyze multiple omics datasets (transcriptomics, proteomics, epigenomics, genomics, metabolomics) for systems biology and precision medicine. Performs cross-omics correlation, multi-omi

Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms. Performs spatial clustering, domain i

Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic lethal interactions,

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, prioritiz

Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Processes LC-MS, GC-MS, NMR data from targeted and untargeted experiments. Performs

Analyze mass spectrometry proteomics data including protein quantification, differential expression, post-translational modifications (PTMs), and protein-protein interactions. Processes MaxQuant, Spec

Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via do

Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pha

Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates actionable reports with candidate compounds, ADMET profiles, and synthesis feasibil

Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expression, variants, drug interactions, and literature. Fe