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UserVibe-Skills is an all-in-one AI skills package. It seamlessly integrates expert-level capabilities and context management into a general-purpose skills package， enabling any AI agent to instantly upgrade its functionality—eliminating the friction of fragmented tools and complex harnesses.
Categories
Indexed Skills (342)
autonomous-builder
Full-stack autonomous software development agent: handles design, implementation, testing, and deployment end-to-end. Auto-activates for project creation, feature development, bug fixing, code refactoring, or when user requests 'build', 'create', 'implement', 'develop', 'fix', or 'refactor' any software project.
benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
bgpt-paper-search
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.
clinical-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.
creating-data-visualizations
Generate plots, charts, and graphs from data with automatic visualization type selection. Use when requesting "visualization", "plot", "chart", or "graph". Trigger with phrases like 'generate', 'create', or 'scaffold'.
cs-foundations
Master discrete mathematics, logic, formal proofs, and computational thinking. Build the mathematical foundation for all computer science.
detecting-performance-regressions
Automatically detect performance regressions in CI/CD pipelines by comparing metrics against baselines. Use when validating builds or analyzing performance trends. Trigger with phrases like "detect performance regression", "compare performance metrics", or "analyze performance degradation".
engineering-features-for-machine-learning
Execute create, select, and transform features to improve machine learning model performance. Handles feature scaling, encoding, and importance analysis. Use when asked to "engineer features" or "select features". Trigger with relevant phrases based on skill purpose.
evaluating-code-models
Evaluates code generation models across HumanEval, MBPP, MultiPL-E, and 15+ benchmarks with pass@k metrics. Use when benchmarking code models, comparing coding abilities, testing multi-language support, or measuring code generation quality. Industry standard from BigCode Project used by HuggingFace leaderboards.
evaluating-llms-harness
Evaluates LLMs across 60+ academic benchmarks (MMLU, HumanEval, GSM8K, TruthfulQA, HellaSwag). Use when benchmarking model quality, comparing models, reporting academic results, or tracking training progress. Industry standard used by EleutherAI, HuggingFace, and major labs. Supports HuggingFace, vLLM, APIs.
evaluating-machine-learning-models
Build this skill allows AI assistant to evaluate machine learning models using a comprehensive suite of metrics. it should be used when the user requests model performance analysis, validation, or testing. AI assistant can use this skill to assess model accuracy, p... Use when appropriate context detected. Trigger with relevant phrases based on skill purpose.
explaining-machine-learning-models
Build this skill enables AI assistant to provide interpretability and explainability for machine learning models. it is triggered when the user requests explanations for model predictions, insights into feature importance, or help understanding model behavior... Use when appropriate context detected. Trigger with relevant phrases based on skill purpose.
generate-image
Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.
generating-test-reports
Generate comprehensive test reports with metrics, coverage, and visualizations. Use when performing specialized testing. Trigger with phrases like "generate test report", "create test documentation", or "show test metrics".
hive-mind-advanced
Advanced Hive Mind collective intelligence system for queen-led multi-agent coordination with consensus mechanisms and persistent memory
hypothesis-generation
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
hypothesis-testing
Property-based testing with Hypothesis for discovering edge cases and validating invariants. Use when implementing comprehensive test coverage, testing complex logic with many inputs, or validating mathematical properties and invariants across input domains. Triggered by: hypothesis, property-based testing, @given, strategies, generative testing.
literature-review
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
markdown-mermaid-writing
Comprehensive markdown and Mermaid diagram writing skill that establishes text-based diagrams as the DEFAULT documentation standard. Use this skill when creating ANY scientific document, report, analysis, or visualization — it ensures all outputs are in version-controlled, token-efficient markdown with embedded Mermaid diagrams as the source of truth, with clear pathways to downstream Python or AI-generated images. Includes full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates ready to use.
market-research-reports
Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix.
markitdown
Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
math
Unified math capabilities - computation, solving, and explanation. I route to the right tool.
matlab
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.
paper-2-web
This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.
peer-review
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.
performing-regression-analysis
Execute this skill empowers AI assistant to perform regression analysis and modeling using the regression-analysis-tool plugin. it analyzes datasets, generates appropriate regression models (linear, polynomial, etc.), validates the models, and provides performa... Use when analyzing code or data. Trigger with phrases like 'analyze', 'review', or 'examine'.
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 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.
planning-with-files
Implements Manus-style file-based planning for complex tasks. Creates task_plan.md, findings.md, and progress.md. Use when starting complex multi-step tasks, research projects, or any task requiring >5 tool calls.
pptx-posters
Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.
preprocessing-data-with-automated-pipelines
Process automate data cleaning, transformation, and validation for ML tasks. Use when requesting "preprocess data", "clean data", "ETL pipeline", or "data transformation". Trigger with relevant phrases based on skill purpose.
property-based-testing
Property-based testing with fast-check (TypeScript/JavaScript) and Hypothesis (Python). Generate test cases automatically, find edge cases, and test mathematical properties. Use when user mentions property-based testing, fast-check, Hypothesis, generating test data, QuickCheck-style testing, or finding edge cases automatically.
providing-performance-optimization-advice
Provide comprehensive prioritized performance optimization recommendations for frontend, backend, and infrastructure. Use when analyzing bottlenecks or seeking improvement strategies. Trigger with phrases like "optimize performance", "improve speed", or "performance recommendations".
prowler-docs
Prowler documentation style guide and writing standards. Trigger: When writing documentation for Prowler features, tutorials, or guides.
pyzotero
Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.
research-grants
Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.
running-clustering-algorithms
Analyze datasets by running clustering algorithms (K-means, DBSCAN, hierarchical) to identify data groups. Use when requesting "run clustering", "cluster analysis", or "group data points". Trigger with relevant phrases based on skill purpose.
scientific-critical-thinking
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
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.
skypilot-multi-cloud-orchestration
Multi-cloud orchestration for ML workloads with automatic cost optimization. Use when you need to run training or batch jobs across multiple clouds, leverage spot instances with auto-recovery, or optimize GPU costs across providers.
sparse-autoencoder-training
Provides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.
splitting-datasets
Process split datasets into training, validation, and testing sets for ML model development. Use when requesting "split dataset", "train-test split", or "data partitioning". Trigger with relevant phrases based on skill purpose.
statistics-math
Statistics, probability, linear algebra, and mathematical foundations for data science
tensorboard
Visualize training metrics, debug models with histograms, compare experiments, visualize model graphs, and profile performance with TensorBoard - Google's ML visualization toolkit
timesfm-forecasting
Zero-shot time series forecasting with Google's TimesFM foundation model. Use this skill when forecasting ANY univariate time series — sales, sensor readings, stock prices, energy demand, patient vitals, weather, or scientific measurements — without training a custom model. Automatically checks system RAM/GPU before loading the model, supports CSV/DataFrame/array inputs, and returns point forecasts with calibrated prediction intervals. Includes a preflight system checker script that MUST be run before first use to verify the machine can load the model. For classical statistical time series models (ARIMA, SARIMAX, VAR) use statsmodels; for time series classification/clustering use aeon.
training-machine-learning-models
Build train machine learning models with automated workflows. Analyzes datasets, selects model types (classification, regression), configures parameters, trains with cross-validation, and saves model artifacts. Use when asked to "train model" or "evalua... Trigger with relevant phrases based on skill purpose.
transformer-lens-interpretability
Provides guidance for mechanistic interpretability research using TransformerLens to inspect and manipulate transformer internals via HookPoints and activation caching. Use when reverse-engineering model algorithms, studying attention patterns, or performing activation patching experiments.
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.
verification--quality-assurance
Comprehensive truth scoring, code quality verification, and automatic rollback system with 0.95 accuracy threshold for ensuring high-quality agent outputs and codebase reliability.
weights-and-biases
Track ML experiments with automatic logging, visualize training in real-time, optimize hyperparameters with sweeps, and manage model registry with W&B - collaborative MLOps platform
anomaly-detector
Anomaly Detector - Auto-activating skill for Data Analytics. Triggers on: anomaly detector, anomaly detector Part of the Data Analytics skill category.
confusion-matrix-generator
Confusion Matrix Generator - Auto-activating skill for ML Training. Triggers on: confusion matrix generator, confusion matrix generator Part of the ML Training skill category.
correlation-analyzer
Correlation Analyzer - Auto-activating skill for Data Analytics. Triggers on: correlation analyzer, correlation analyzer Part of the Data Analytics skill category.
data-normalization-tool
Data Normalization Tool - Auto-activating skill for ML Training. Triggers on: data normalization tool, data normalization tool Part of the ML Training skill category.
data-quality-checker
Data Quality Checker - Auto-activating skill for Data Pipelines. Triggers on: data quality checker, data quality checker Part of the Data Pipelines skill category.
detecting-data-anomalies
Process identify anomalies and outliers in datasets using machine learning algorithms. Use when analyzing data for unusual patterns, outliers, or unexpected deviations from normal behavior. Trigger with phrases like "detect anomalies", "find outliers", or "identify unusual patterns".
feature-importance-analyzer
Feature Importance Analyzer - Auto-activating skill for ML Training. Triggers on: feature importance analyzer, feature importance analyzer Part of the ML Training skill category.
metric-calculator
Metric Calculator - Auto-activating skill for Data Analytics. Triggers on: metric calculator, metric calculator Part of the Data Analytics skill category.
regression-analysis-helper
Regression Analysis Helper - Auto-activating skill for Data Analytics. Triggers on: regression analysis helper, regression analysis helper Part of the Data Analytics skill category.
unsloth
Expert guidance for fast fine-tuning with Unsloth - 2-5x faster training, 50-80% less memory, LoRA/QLoRA optimization
visualization-best-practices
Visualization Best Practices - Auto-activating skill for Data Analytics. Triggers on: visualization best practices, visualization best practices Part of the Data Analytics skill category.
skill-installer
Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos).
lqf_machine_learning_expert_guide
LQF Machine Learning Expert Guide - Auto-activating skill for ML/Statistical Modeling with Critical Discussion Mode. Triggers on: machine learning, modeling, prediction, training, classification, regression, clustering, deep learning, neural network, model evaluation, feature engineering, hyperparameter tuning, overfitting, underfitting, baseline, ablation study, critique my approach, review my model, is this a good idea, should I use, what's wrong with, evaluate my solution, challenge my assumptions, discuss my approach Engages in critical discussion with minimum 3 rounds of iterative refinement. Challenges both user proposals and own suggestions with fact-based critique. Demands evidence and baselines before accepting solutions.
algorithmic-art
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
alpha-vantage
Access real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API. Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, options data, market news/sentiment, insider transactions, GDP, CPI, treasury yields, gold/silver/oil prices, Bitcoin/crypto prices, forex exchange rates, or calculating technical indicators (SMA, EMA, MACD, RSI, Bollinger Bands). Requires a free API key from alphavantage.co.
arboreto
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
astropy
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
biorxiv-database
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
chembl-database
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
cirq
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.
clinicaltrials-database
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
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.
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
create-plan
Create a concise plan. Use when a user explicitly asks for a plan related to a coding task.
data-artist
Create beautiful data visualizations with mathematical elegance, color theory, and narrative design - the "Data is Beautiful" aesthetic.
data-exploration-visualization
自动化数据探索和可视化工具，提供从数据加载到专业报告生成的完整EDA解决方案。支持多种图表类型、智能数据诊断、建模评估和HTML报告生成。适用于医疗、金融、电商等领域的数据分析项目。
datacommons-client
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.
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
deepchem
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
digital-brain
This skill should be used when the user asks to "write a post", "check my voice", "look up contact", "prepare for meeting", "weekly review", "track goals", or mentions personal brand, content creation, network management, or voice consistency.
docs-review
Review documentation changes for compliance with the Metabase writing style guide. Use when reviewing pull requests, files, or diffs containing documentation markdown files.
docs-write
Write documentation following Metabase's conversational, clear, and user-focused style. Use when creating or editing documentation files (markdown, MDX, etc.).
docx
Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction. When Claude needs to work with professional documents (.docx files) for: (1) Creating new documents, (2) Modifying or editing content, (3) Working with tracked changes, (4) Adding comments, or any other document tasks
pptx
Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
edgartools
Python library for accessing, analyzing, and extracting data from SEC EDGAR filings. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly reports (10-K, 10-Q), proxy statements (DEF 14A), 8-K current events, company screening by ticker/CIK/industry, multi-period financial analysis, or any SEC regulatory filings.
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
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.
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.
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.
fred-economic-data
Query FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources. Access GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, and academic research requiring U.S. and international economic indicators.
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.
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.
geomaster
Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, and 7 programming languages (Python, R, Julia, JavaScript, C++, Java, Go) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modeling, marine spatial analysis, atmospheric science, and any geospatial computation task.
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.
get-available-resources
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
gradient-methods
Problem-solving strategies for gradient methods in optimization
Showing top 100 of 342 skills by quality score. Browse the full catalog at /browse.
Bio shown is the top-scored skill's repo description as a fallback — real GitHub bios land in a future update.