Claude Skills by FreedomIntelligence

--> --- name: 'fhir-development' description: 'FHIR Development agent for healthcare workflows.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill implements the FHIR Development workflow using Anthropic's Claude.

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 remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.

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

--> --- name: 'gene-panel-design-agent' description: 'AI-powered design of targeted gene panels for clinical and research applications including cancer diagnostics, pharmacogenomics, and rare disease testing.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Gene Panel Design Agent** provides AI-driven design of targeted sequencing panels for clinical diagnostics, cancer profiling, pharmacogen...

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture

Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or optimization), generate fluorescent pixel art, or interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows.

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, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design.

Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes.

Compassionate bereavement support, memorial creation, grief education, and healing journey guidance. Specializes in understanding grief stages, creating meaningful tributes, and supporting

Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.

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, understanding tissue-specific expression, and interpreting non-coding variant effects.

Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.

Calculate polygenic risk scores from DTC genetic data using the PGS Catalog

--> --- name: 'hemoglobinopathy-analysis-agent' description: 'AI-powered analysis of hemoglobin disorders including sickle cell disease, thalassemias, and variant hemoglobins using HPLC, electrophoresis, and molecular data.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Hemoglobinopathy Analysis Agent** provides comprehensive AI-driven analysis of hemoglobin disorders. It integrates HPLC ch...

Ensure HIPAA compliance when handling PHI (Protected Health Information). Use when writing code that accesses user health data, check-ins, journal entries, or any sensitive information. Activates

--> --- name: 'hrd-analysis-agent' description: 'AI-powered homologous recombination deficiency (HRD) analysis for PARP inhibitor response prediction using genomic scarring signatures and BRCA pathway assessment.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **HRD Analysis Agent** provides comprehensive analysis of homologous recombination deficiency for predicting response to PARP inhibitor...

Heart rate variability biometrics and emotional awareness training. Expert in HRV analysis, interoception training, biofeedback, and emotional intelligence. Activate on 'HRV', 'heart rate variability',

Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.

--> --- name: 'immune-checkpoint-combination-agent' description: 'AI-powered analysis for predicting optimal immune checkpoint inhibitor combinations based on tumor microenvironment, biomarkers, and molecular profiling.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Immune Checkpoint Combination Agent** analyzes tumor molecular profiles to predict optimal immune checkpoint inhibitor (ICI) c...

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 10 infographic types, 8 industry styles, and colorblind-safe palettes.

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, domain architecture analysis, evolutionary classification, and GO term mapping.

Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use wh...

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 regulatory genomics, motif analysis, and GWAS regulatory variant interpretation.

Expert in Jungian analytical psychology, depth psychology, shadow work, archetypal analysis, dream interpretation, active imagination, addiction/recovery through Jungian lens, and the individuation

Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.

--> --- name: knowledge-synthesis description: Combines search results from multiple sources into coherent, deduplicated answers with source attribution. Handles confidence scoring based on freshness and authority, and summarizes large result sets effectively. keywords: - synthesis - deduplication - summarization - answers - reporting measurable_outcome: Produces a single coherent answer from >5 diverse sources with clear attribution and <10% duplication. allowed-tools: - read_file - run_shel...

--> --- name: kragen-knowledge-graph description: Graph-RAG Solver keywords: - knowledge-graph - RAG - reasoning - graph-of-thoughts - biomedical-qa measurable_outcome: Return a reasoning path and an answer supported by ≥3 knowledge graph nodes for complex biomedical questions with <5s latency. license: MIT metadata: author: Bioinformatics Oxford version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - web_fetch --- A knowledge graph-enhanced Retrieval-Augmen...

--> --- name: 'lab-results' description: 'Lab Results agent for healthcare workflows.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill implements the Lab Results workflow using Anthropic's Claude.

Interact with the Labstep electronic lab notebook API using labstepPy. Query experiments, protocols, resources, inventory, and other lab entities.

Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.

--> --- name: leads-literature-mining description: Review Automator keywords: - literature-mining - systematic-review - meta-analysis - pubmed - evidence-synthesis measurable_outcome: Complete a systematic review screen of 100+ papers with >90% inclusion/exclusion accuracy compared to human baseline. license: CC-BY-4.0 metadata: author: Nature Communications 2025 version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - web_fetch --- A specialized LLM agent fo...

Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding pocket optimization, (4) Metal coordination site design, (5) Cofactor binding proteins. For standard protein design, use proteinmpnn. For solubility optimization, use solublempnn.

Select and configure linear solvers for systems Ax=b in dense and sparse problems. Use when choosing direct vs iterative methods, diagnosing convergence issues, estimating conditioning, selecting preconditioners, or debugging stagnation in GMRES/CG/BiCGSTAB.

--> --- name: 'liquid-biopsy-analytics-agent' description: 'Comprehensive analysis of liquid biopsy data (ctDNA, CTCs) for cancer detection, MRD monitoring, and response tracking.' keywords: - liquid-biopsy - ctdna - mrd - cancer-detection - treatment-response measurable_outcome: 'Detects circulating tumor DNA with 0.01% sensitivity and accurately predicts treatment response in longitudinal samples.' allowed-tools: - read_file - run_shell_command --- The **Liquid Biopsy Analytics Agent** prov...

Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.

Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by Valyu semantic search.

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 for papers/datasets, or working with H5AD, CSV, GEO/SRA accessions, or biological data. Requires lobster-ai package installed.

--> --- name: 'long-read-sequencing-agent' description: 'AI-powered analysis of long-read sequencing data (PacBio, ONT) for structural variant detection, isoform discovery, epigenetic modifications, and de novo assembly.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Long-Read Sequencing Agent** provides comprehensive AI-driven analysis of long-read sequencing data from PacBio (HiFi) and Ox...

--> --- name: mage-antibody-generator description: Ab seq forge keywords: - antibody - antigen - FASTA - generation - validation measurable_outcome: Generate the requested number of antibody sequences (default ≥5) with metadata (model checkpoint, seed) and deliver FASTA files within 10 minutes. license: MIT metadata: author: MAGE Team version: "1.0.0" compatibility: - system: Python 3.9+ / GPU allowed-tools: - run_shell_command - read_file --- Run the MAGE antibody generation workflow to prop...

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 standard with full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates.

Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.

Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.

An AI agent for therapeutic discovery that executes transparent, multi-step omics analyses including research planning, code execution, and literature reasoning.

Extract medical entities (symptoms, medications, lab values, diagnoses) from patient messages.

Write comprehensive literature reviews for medical imaging AI research. Use when writing survey papers, systematic reviews, or literature analyses on topics like segmentation, detection, classification in CT, MRI, X-ray, ultrasound, or pathology imaging. Triggers on requests for "review paper", "survey", "literature review", "综述", "systematic review", or mentions of writing academic reviews on deep learning for medical imaging.

Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research. Access ChEMBL, PubMed, ClinicalTrials.gov, OpenTargets, OpenFDA, OMIM, Reactome, KEGG, UniProt, and more through a unified MCP endpoint. Use when researching disease targets, finding approved/investigational drugs, searching clinical evidence, discovering genetic associations, or analyzing compound bioactivity data.

Generate daily or on-demand medical research briefs for any medical specialty. Searches latest research from top-tier journals, delivers concise summaries with 1-sentence takeaways, images when available, and direct links. Use when user asks for medical news, research updates, journal briefs, or specialty-specific medical updates for specialties like endocrinology, cardiology, oncology, neurology, etc.

Search medRxiv medical preprints with natural language queries. Powered by Valyu semantic search.

Plan and evaluate mesh generation for numerical simulations. Use when choosing grid resolution, checking aspect ratios/skewness, estimating mesh quality constraints, or planning adaptive mesh refinement for PDE discretization.

--> --- name: 'microbiome-cancer-agent' description: 'AI-powered analysis of microbiome-cancer interactions including tumor microbiome profiling, immunotherapy response prediction, and microbiome-targeted therapeutic opportunities.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Microbiome-Cancer Interaction Agent** analyzes relationships between the microbiome and cancer, including tumor-as...