Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.
Use when you've developed a broadly useful skill and want to contribute it upstream via pull request - guides process of branching, committing, pushing, and creating PR to contribute skills back...
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets,...
Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate...
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...
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for...
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
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Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Use when errors occur deep in execution and you need to trace back to find the original trigger - systematically traces bugs backward through call stack, adding instrumentation when needed, to...
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified...
Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures...
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),...
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,...
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of...
Use when about to claim work is complete, fixed, or passing, before committing or creating PRs - requires running verification commands and confirming output before making any success claims;...
Automated network troubleshooting and diagnostics for WSL/Linux environments