Claude Skills by FreedomIntelligence

--> --- name: chemistry-agent description: Autonomous chemical synthesis & analysis keywords: - chemistry - synthesis - molecules - reaction - lab-automation measurable_outcome: Successfully plans valid synthesis routes for 90% of target small molecules. license: MIT metadata: author: Biomedical OS Team version: "1.0.0" compatibility: - system: Python 3.10+ allowed-tools: - run_shell_command - read_file - write_file --- The Chemistry Agent is a specialized module for autonomous chemical reaso...

--> --- name: 'chip-clonal-hematopoiesis-agent' description: 'AI-powered clonal hematopoiesis of indeterminate potential (CHIP) detection, risk stratification, and cardiovascular/malignancy risk prediction using genomic and clinical data.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **CHIP Clonal Hematopoiesis Agent** provides comprehensive detection and risk stratification of clonal hemato...

--> --- name: 'chromosomal-instability-agent' description: 'AI-powered analysis of chromosomal instability (CIN) signatures for cancer prognosis, immunotherapy response prediction, and therapeutic vulnerability identification.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Chromosomal Instability Agent** analyzes CIN signatures to predict cancer prognosis, immunotherapy response, and therap...

--> --- name: 'claims-appeals' description: 'Claims Appeals 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 Claims Appeals workflow using Anthropic's Claude.

Ancestry decomposition PCA against the Simons Genome Diversity Project

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

Semantic Similarity Index for disease research literature using PubMedBERT embeddings

Identify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application. For diagnostic reasoning, treatment decisions, and

--> --- name: 'clinical-nlp-extractor' description: 'Extracts medical entities (Diseases, Medications, Procedures) from unstructured clinical text using regex and simple rules (or LLM wrappers).' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Clinical NLP Skill** converts free-text clinical notes into structured data. It identifies key medical entities like problems/diagnoses, medications, a...

--> --- name: clinical-note-summarization description: Structure raw clinical notes into SOAP-format summaries with explicit contradictions, missing data, and ICD-linked assessments using the provided prompt + usage script. allowed-tools: - read_file - run_shell_command ---

Search ClinicalTrials.gov with natural language queries. Find clinical trials, enrollment, and outcomes using Valyu semantic search.

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

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

--> --- name: 'cnv-caller-agent' description: 'AI-enhanced copy number variation calling and analysis from sequencing data for cancer genomics, constitutional CNV detection, and chromosomal aberration characterization.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **CNV Caller Agent** provides comprehensive AI-enhanced copy number variation analysis from WGS, WES, and targeted sequencing for...

--> --- name: 'coagulation-thrombosis-agent' description: 'AI-powered analysis of coagulation disorders, thrombosis risk prediction, anticoagulation management, and platelet function assessment using machine learning.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Coagulation and Thrombosis Agent** provides AI-driven analysis of hemostatic disorders, thrombosis risk assessment, and anticoag...

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

--> --- name: compbioagent-explorer description: scRNA-seq Explorer keywords: - single-cell - visualization - web-app - cellxgene - exploration measurable_outcome: Launch a local web instance for interactive scRNA-seq exploration and generate 3+ custom visualizations per session. license: MIT metadata: author: CompBioAgent Team version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - web_fetch --- An LLM-powered web application for single-cell RNA-seq data ex...

--> --- name: computational-pathology-agent description: Analyze Whole Slide Images (WSI) for digital pathology, including tissue segmentation and feature extraction. keywords: - wsi - digital-pathology - deep-learning - resnet - openslide measurable_outcome: Preprocess and extract tissue patches from a 1GB+ .svs slide within 15 minutes for downstream ML tasks. license: MIT metadata: author: MD BABU MIA, PhD version: "1.0.0" compatibility: - system: python 3.9+ allowed-tools: - run_shell_comm...

Spatial and temporal convergence analysis with Richardson extrapolation and Grid Convergence Index (GCI) for solution verification

Detect crisis signals in user content using NLP, mental health sentiment analysis, and safe intervention protocols. Implements suicide ideation detection, automated escalation, and crisis resource

Handle mental health crisis situations in AI coaching safely. Use when implementing crisis detection, safety protocols, emergency escalation, or suicide prevention features. Activates for crisis

--> --- name: crispr-guide-design description: Guide foundry keywords: - CRISPR - sgRNA - Doench - off-target - oligos measurable_outcome: Return the requested number of guides (default ≥4) with efficiency + specificity scores, coordinates, and cloning oligos within 10 minutes per gene. license: MIT metadata: author: CRISPR-GPT Team version: "1.0.0" compatibility: - system: Python 3.10+ allowed-tools: - run_shell_command - read_file --- Automate sgRNA selection, scoring, off-target evaluation...

--> --- name: 'crispr-offtarget-predictor' description: 'Predicts potential off-target sites for a given sgRNA sequence using mismatch analysis.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill identifies potential off-target binding sites for a specific sgRNA sequence. It helps researchers assess the specificity of their CRISPR design.

--> --- name: 'cryoem-ai-drug-design-agent' description: '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.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Cryo-EM AI Drug Design Agent** integrates cryo-electron microscopy structural data with AlphaFold3, generative A...

--> --- name: 'ctdna-dynamics-mrd-agent' description: 'AI-powered circulating tumor DNA dynamics analysis for molecular residual disease detection, treatment response monitoring, and early relapse prediction using liquid biopsy.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **ctDNA Dynamics MRD Agent** provides comprehensive analysis of circulating tumor DNA dynamics for molecular residual d...

--> --- name: 'cytokine-storm-analysis-agent' description: 'AI-powered cytokine release syndrome (CRS) and cytokine storm analysis for prediction, monitoring, and management in immunotherapy and infectious disease.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Cytokine Storm Analysis Agent** provides comprehensive AI-driven analysis of cytokine release syndrome (CRS) and hyperinflammatory ...

Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.

Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

--> --- name: data-visualization-biomedical description: "Publication-quality visualizations for biomedical and genomics data. Use when creating volcano plots, heatmaps, UMAP plots, dot plots, survival curves, forest plots, or multi-panel figures. Includes scanpy, matplotlib, seaborn, plotly workflows with journal-ready aesthetics and proper statistical annotations." license: Proprietary ---

--> --- name: data-visualization-expert description: Generate insightful, publication-quality visualizations from complex datasets. keywords: - charts - plots - analysis - pandas - matplotlib - seaborn measurable_outcome: Create 3 high-resolution (300dpi) statistical plots (volcano, heatmap, scatter) within 15 minutes. license: MIT metadata: author: AI Agentic Skills Team version: "2.0.0" compatibility: - system: linux, macos allowed-tools: - run_shell_command - write_file - read_file --- A d...

Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities.

--> --- name: deep-research-swarm description: Multi-agent research literature analysis keywords: - research - literature - swarm - multi-agent - hypothesis measurable_outcome: Generates comprehensive literature review with >50 citations in <5 minutes. license: MIT metadata: author: Biomedical OS Team version: "1.0.0" compatibility: - system: Python 3.10+ allowed-tools: - run_shell_command - read_file - google_web_search --- A coordinated swarm of agents designed to perform deep, parallelized...

Execute autonomous multi-step deep research on any topic. Use when the user asks for comprehensive research, literature reviews, competitive analysis, topic deep-dives, or wants to understand a complex subject from multiple angles. Triggers on "deep research", "research on", "investigate", "literature review", "comprehensive analysis", "what do we know about", "summarize research on".

--> --- name: 'deep-visual-proteomics-agent' description: 'AI-driven integration of cellular imaging, laser microdissection, and ultra-sensitive mass spectrometry for spatially-resolved single-cell proteomics.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Deep Visual Proteomics Agent** implements the Deep Visual Proteomics (DVP) workflow that combines AI-driven image analysis of cellular p...

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.

Select and apply numerical differentiation schemes for PDE/ODE discretization. Use when choosing finite difference/volume/spectral schemes, building stencils, handling boundaries, estimating truncation error, or analyzing dispersion and dissipation.

--> --- name: 'digital-twin-clinical-agent' description: 'AI-powered patient digital twin creation for clinical trial simulation, treatment outcome prediction, and personalized medicine using real-world data and multi-omics integration.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Digital Twin Clinical Agent** creates AI-powered virtual replicas of individual patients by integrating genom...

End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu.

--> --- name: 'drug-interaction-checker' description: 'Checks for potential drug-drug interactions (DDIs) between a list of medications.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill analyzes a list of medications to identify known interactions, focusing on safety and contraindications.

Search FDA drug labels with natural language queries. Official drug information, indications, and safety data via Valyu.

Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance

Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu.

--> --- name: 'ehr-fhir-integration' description: 'Provides comprehensive tools for working with Electronic Health Records (EHR) using the HL7 FHIR standard.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **EHR/FHIR Integration Skill** enables AI agents to interact with FHIR servers to search, read, and analyze clinical data.

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

Analyzes disease patterns and health events through epidemiological lens using surveillance systems, outbreak investigation methods, and disease modeling frameworks. Provides insights on disease spread, risk factors, prevention strategies, and public health interventions. Use when: Disease outbreaks, health policy evaluation, risk assessment, intervention planning. Evaluates: Transmission dynamics, risk factors, causality, population health impact, intervention effectiveness.

--> --- name: 'epigenomics-methylgpt-agent' description: 'AI-powered DNA methylation analysis using MethylGPT foundation models for epigenomic profiling, differential methylation detection, and cancer epigenome characterization.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Epigenomics MethylGPT Agent** leverages foundation models for comprehensive DNA methylation analysis. It integrates M...

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.

--> --- name: 'exosome-ev-analysis-agent' description: 'AI-powered extracellular vesicle and exosome analysis for cancer biomarker discovery, liquid biopsy applications, and intercellular communication profiling.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Exosome/EV Analysis Agent** provides comprehensive AI-driven analysis of extracellular vesicles for cancer biomarker discovery, liqui...

Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.

FHIR API development guide for building healthcare endpoints. Use when: (1) Creating FHIR REST endpoints (Patient, Observation, Encounter, Condition, MedicationRequest), (2) Validating FHIR resources and returning proper HTTP status codes and error responses, (3) Implementing SMART on FHIR authorization and OAuth scopes, (4) Working with Bundles, transactions, batch operations, or search pagination. Covers FHIR R4 resource structures, required fields, value sets (status codes, gender, intent)...