reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
fda-database
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
scikit-survival
Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival library.
scikit-learn
Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
scientific-writing
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
pyhealth
Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).
pydicom
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
pufferlib
This skill should be used when working with reinforcement learning tasks including high-performance RL training, custom environment development, vectorized parallel simulation, multi-agent systems, or integration with existing RL environments (Gymnasium, PettingZoo, Atari, Procgen, etc.). Use this skill for implementing PPO training, creating PufferEnv environments, optimizing RL performance, or developing policies with CNNs/LSTMs.
pubmed-database
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
protocolsio-integration
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
polars
Fast DataFrame library (Apache Arrow). Select, filter, group_by, joins, lazy evaluation, CSV/Parquet I/O, expression API, for high-performance data analysis workflows.
plotly
Interactive scientific and statistical data visualization library for Python. Use when creating charts, plots, or visualizations including scatter plots, line charts, bar charts, heatmaps, 3D plots, geographic maps, statistical distributions, financial charts, and dashboards. Supports both quick visualizations (Plotly Express) and fine-grained customization (graph objects). Outputs interactive HTML or static images (PNG, PDF, SVG).
pennylane
Cross-platform Python library for quantum computing, quantum machine learning, and quantum chemistry. Enables building and training quantum circuits with automatic differentiation, seamless integration with PyTorch/JAX/TensorFlow, and device-independent execution across simulators and quantum hardware (IBM, Amazon Braket, Google, Rigetti, IonQ, etc.). Use when working with quantum circuits, variational quantum algorithms (VQE, QAOA), quantum neural networks, hybrid quantum-classical models, molecular simulations, quantum chemistry calculations, or any quantum computing tasks requiring gradient-based optimization, hardware-agnostic programming, or quantum machine learning workflows.
peer-review
Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.
labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
clinvar-database
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.
kegg-database
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.
hypothesis-generation
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
hypogenic
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 hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.
geopandas
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.
geo-database
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.
geniml
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
generate-image
Generate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that isn't a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.
gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
fluidsim
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
flowio
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
academic-chapter-writer
Comprehensive academic textbook chapter writing system for medical/scientific content. Use when the user wants to: (1) Write a full textbook chapter (5,000-15,000 words) on any medical/scientific topic, (2) Generate a detailed table of contents with section word counts, (3) Research topics via PubMed MCP and compile 20-30 references, (4) Write section-by-section with proper citations in Vancouver format, (5) Create publishable academic content with Eric Topol-inspired voice and authentic human prose, (6) Get approval at TOC stage before writing begins, (7) Export well-structured chapters for textbook publication.
article-extractor
Extract clean article content from URLs (blog posts, articles, tutorials) and save as readable text. Use when user wants to download, extract, or save an article/blog post from a URL without ads, navigation, or clutter.
authentic-voice
Transform AI-sounding writing into natural, human prose. Use when creating or editing any written content—articles, essays, reports, emails, social posts, scripts, or marketing copy—to avoid patterns that signal AI authorship. Triggers on requests to "make it sound human," "less AI," "more natural," improve voice/tone, or any writing task where authentic style matters.
browser-automation
Browser automation for ChatGPT Plus and Gemini Advanced web interfaces. Uses Playwright MCP to interact with your paid subscriptions without API costs. Supports both models for writing comparison.
cardiology-content-repurposer
Transform long-form cardiology content (YouTube transcripts, newsletters, PDFs, knowledge bases) into high-quality thought leadership content across multiple formats. Use when the user wants to repurpose medical/cardiology content into: (1) Short newspaper articles (Inshorts style), (2) Atomic essays, (3) Tweets, (4) Twitter threads, or (5) Medium-style blogs. Maintains authentic interventional cardiologist voice with clinical authority, uses 4A framework, targets specific patient archetypes, and leverages PubMed for evidence-based citations when needed.
exploratory-data-analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
cardiology-editorial
Comprehensive cardiology editorial writing system for thought leadership newsletters. Use when the user wants to: (1) Identify and score recent landmark trials from top cardiology journals (NEJM, JAMA, Lancet, JACC, EHJ, etc.), (2) Write evidence-based editorials in Eric Topol's style from Ground Truth, (3) Create 500-word commentaries on clinical trials with PubMed citations, (4) Analyze trial importance using hybrid rules + LLM scoring, (5) Write editorials from full papers OR abstract-only scenarios, (6) Build thought leadership content for cardiologists, or (7) Synthesize recent cardiology advances for peers and referring physicians.
cardiology-newsletter-writer
Create evidence-based cardiology newsletters for thought leadership in Eric Topol's authoritative Ground Truths style. Use when the user wants to analyze trending medical topics with engagement predictions, conduct data-driven topic selection, research medical literature using PubMed, or write comprehensive well-referenced newsletters that build professional authority as an interventional cardiologist. Handles complete workflow from trend analysis to final draft with smooth analytical flow between topics.
cardiology-science-for-people
Write rigorous, accurate cardiology science for general audiences—not doctors. Use when the user wants to: (1) Explain clinical trials or research in plain English, (2) Write science content an 8th grader can understand WITHOUT dumbing it down, (3) Create thought leadership for the intelligent public rather than medical peers, (4) Transform complex cardiology findings into stories and narratives, (5) Write pieces where readers DON'T need another LLM to understand the explanation. Maintains full scientific rigor with PubMed citations for verification while avoiding academic language, trial acronyms, and intimidating statistics.
cardiology-topol-writer
Transform thought dumps into polished cardiology content in Eric Topol's Ground Truths voice. Use when the user wants to write cardiology articles, newsletters, video scripts, or educational content from scattered ideas, clinical observations, or research notes—combining Eric Topol's evidence-based clarity with Peter Attia's deep-dive rigor.
cardiology-trial-editorial
Identify landmark cardiology trials and write evidence-based editorials in Eric Topol's authoritative Ground Truths style. Use when the user wants to: (1) Discover and evaluate recent important trials from top cardiology journals (NEJM, JACC, Lancet, EHJ, Circulation), (2) Assess trial importance using systematic scoring, (3) Write 500-word editorials on cardiology/interventional cardiology advances for physician audiences, (4) Create thought leadership content that demonstrates deep domain expertise. Supports both full-text and abstract-only scenarios with PubMed integration for references.
cardiology-tweet-writer
Generate scientifically accurate, engaging cardiology tweets for thought leadership. Use when creating social media content for a cardiologist targeting patients, health enthusiasts, health optimizers, people with lifestyle diseases, and caregivers. Produces 10 tweets per batch using permutations of cardiology seed ideas and modifiers. Incorporates feedback to improve output quality over time.
cardiology-visual-system
Unified visual content system for cardiology thought leadership. Automatically routes requests to the optimal tool—Fal.ai for blog imagery, Gemini for infographics, Mermaid for flowcharts/pathways, Marp for slides, Plotly for data visualization. One skill handles all visual needs within Claude Code.
parallel-literature-search
Parallel search across PubMed, Perplexity, and your knowledge base. Searches all sources simultaneously and synthesizes findings with citations. Faster evidence gathering for clinical questions.
perplexity-search
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 recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model's knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.
quick-topic-researcher
Rapid topic mastery for video/content prep. Takes a topic → generates 5 research questions → parallel PubMed + web search → outputs McKinsey-style brief in 5 minutes. Use BEFORE recording videos or writing content.
social-media-trends-research
Programmatic social media and marketing research using free tools: pytrends (Google Trends), yars (Reddit without API keys), and Perplexity MCP (Twitter/TikTok/Web). Use when finding trending topics in a niche, tracking keyword velocity and volume, monitoring Reddit discussions, discovering what's going viral, or researching content opportunities before writing. Zero-cost research stack with built-in rate limiting. Complements content-marketing-social-listening skill with executable code.
twitter-longform-medical
Write data-driven, evidence-first long-form Twitter posts on medicine and cardiology. Use when the user wants to: (1) Create thought leadership content in the style of Eric Topol, Peter Attia, Andrew Huberman, or Rhonda Patrick, (2) Present clinical evidence with charts, data, and Q1 journal citations for educated non-specialist audiences, (3) Write confident, matter-of-fact medical content that is rigorous without being inaccessible, (4) Explain trials, drugs, or medical phenomena using data visualization and systematic evidence review, (5) Build authority through methodological rigor and clear conclusions backed by evidence. NOT for newsletters or Substack. For Twitter long-form posts only.
video-delivery-coach
Analyze YOUR video recordings before publishing. Evaluates voice (pace, pitch, volume), facial expressions (emotions, eye contact, smiles), and content (filler words, structure). Helps improve your Hinglish YouTube delivery over time.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
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