research-lookup
Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations.
scanpy
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
scientific-brainstorming
Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.
scientific-critical-thinking
Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.
scientific-schematics
Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
scientific-slides
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
scientific-visualization
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
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.
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.
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-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.
scvi-tools
This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential expression, cell type annotation, multimodal integration, and spatial analysis tasks.
seaborn
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.
shap
Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
stable-baselines3
Use this skill for reinforcement learning tasks including training RL agents (PPO, SAC, DQN, TD3, DDPG, A2C, etc.), creating custom Gym environments, implementing callbacks for monitoring and control, using vectorized environments for parallel training, and integrating with deep RL workflows. This skill should be used when users request RL algorithm implementation, agent training, environment design, or RL experimentation.
statistical-analysis
Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting, for academic research.
statsmodels
Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.
string-database
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
sympy
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
torch-geometric
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
torchdrug
Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets, for PyTorch-based ML on molecules, proteins, and biomedical graphs.
transformers
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
treatment-plans
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.
umap-learn
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
uspto-database
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
vaex
Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that don't fit in memory.
venue-templates
Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.
zarr-python
Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
zinc-database
Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
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.
cardiology-youtube-scriptwriter
End-to-end YouTube content creation for cardiology channels. Use when user wants to create YouTube videos about cardiology, heart health, or cardiovascular topics. Triggers on greetings with content intent, requests for video ideas or scripts, help with cardiology YouTube channels, heart health video content requests, or any cardiology content creation conversation. Handles complete workflow from ideation through social listening, topic selection, and full script delivery.
carousel-generator
Instagram carousel generator. Creates 1080x1080px branded slides from text/markdown input. Use this skill when you need to generate Instagram carousel slides with Dr. Shailesh Singh's brand colors, typography, and footer. Supports both @heartdocshailesh and @dr.shailesh.singh accounts.
content-marketing-social-listening
Comprehensive content marketing toolkit for discovering viral content opportunities, social listening, knowledge gap analysis, and content demand assessment across platforms. Use when researching trending topics in a niche, finding what's going viral, assessing content knowledge gaps, planning content calendars, or identifying high-demand content opportunities. Integrates with perplexity-search for real-time trend data and research-lookup for deep analysis.
content-os
Content OS orchestrator - the master skill that produces ALL content types from one seed idea (forward mode) or splits long-form content into short-form pieces (backward mode). Invokes research, writing, quality review, and visual generation skills in a coordinated pipeline. Long-form content goes through full quality gates; short-form gets quick accuracy pass.
content-reflection
Pre-publication quality assurance for cardiology thought leadership content. Use AFTER any content is drafted to evaluate scientific rigor, voice authenticity, positioning alignment, audience calibration, and credibility risk. Provides structured critique with specific revision suggestions. Works on any content type—tweets, threads, newsletters, editorials, video scripts.
content-research-writer
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section. Transforms your writing process from solo effort to collaborative partnership.
content-seo-optimizer
Three-agent SEO audit pipeline. Scrapes your content → analyzes SERP competitors → generates prioritized optimization report with P0/P1/P2 recommendations. Use BEFORE and AFTER publishing to maximize organic reach.
content-trend-researcher
Advanced content and topic research skill that analyzes trends across Google Analytics, Google Trends, Substack, Medium, Reddit, LinkedIn, X, blogs, podcasts, and YouTube to generate data-driven article outlines based on user intent analysis
cremieux-cardio
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.
deep-researcher
Performs comprehensive, multi-layered research on any topic with structured analysis and synthesis of information from multiple sources. Uses file-based research tracking, parallel investigation threads, and context-efficient patterns for deep investigations. ALL MEDICAL CITATIONS FROM PUBMED MCP ONLY.
ensemble-content-scorer
Multi-model consensus scoring for content ideas. Scores the same idea with Claude, GPT-4o, Gemini, and Grok in parallel, then aggregates for a balanced verdict. Reduces single-model bias and improves viral predictions.
gemini-imagegen
Generate and edit images using the Gemini API (Nano Banana Pro). Use this skill when creating images from text prompts, editing existing images, applying style transfers, generating logos with text, creating stickers, product mockups, or any image generation/manipulation task. Supports text-to-image, image editing, multi-turn refinement, and composition from multiple reference images.
influencer-analyzer
Track and analyze cardiology content creators (Topol, Attia, York Cardiology, Indian channels). Discovers content patterns, topics, engagement, and gap opportunities for your Hinglish content strategy.
infographic-generator
Generate world-class medical infographics using carousel-level visual language. Templates include hero stats, multi-section layouts, comparisons, myth-busters, process flows, and patient checklists. Default 1080x1350 for Instagram.
mcp-management
Manage Model Context Protocol (MCP) servers - discover, analyze, and execute tools/prompts/resources from configured MCP servers. Use when working with MCP integrations, need to discover available MCP capabilities, filter MCP tools for specific tasks, execute MCP tools programmatically, access MCP prompts/resources, or implement MCP client functionality. Supports intelligent tool selection, multi-server management, and context-efficient capability discovery.
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