Components

Find bugs, security vulnerabilities, and code quality issues in local branch changes. Use when asked to review changes, find bugs, security review, or audit code on the current branch.

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.

Search and deploy services from Railway's template marketplace. Use when user wants to add a service from a template, find templates for a specific use case, or deploy tools like Ghost, Strapi, n8n, Minio, Uptime Kuma, etc. For databases (Postgres, Redis, MySQL, MongoDB), prefer the railway-database skill.

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.

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

This skill should be used when the user wants to "create a skill", "add a skill to plugin", "write a new skill", "improve skill description", "organize skill content", or needs guidance on skill structure, progressive disclosure, or skill development best practices for Claude Code plugins.

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.

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.

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.

PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.

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.

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).

Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.

Fast DataFrame library (Apache Arrow). Select, filter, group_by, joins, lazy evaluation, CSV/Parquet I/O, expression API, for high-performance data analysis workflows.

Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working with quantum algorithms, simulations, or quantum hardware including (1) Building quantum circuits with gates and measurements, (2) Running quantum algorithms (VQE, QAOA, Grover), (3) Transpiling/optimizing circuits for hardware, (4) Executing on IBM Quantum or other providers, (5) Quantum chemistry and materials science, (6) Quantum machine learning, (7) Visualizing circuits and results, or (8) Any quantum computing development task.

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

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.

Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting, for academic research.

Iterate on a PR until CI passes. Use when you need to fix CI failures, address review feedback, or continuously push fixes until all checks are green. Automates the feedback-fix-push-wait cycle.

Search Engine Optimization specialist for content strategy, technical SEO, keyword research, and ranking improvements. Use when optimizing website content, improving search rankings, conducting keyword analysis, or implementing SEO best practices. Expert in on-page SEO, meta tags, schema markup, and Core Web Vitals.

Manage Railway deployments - view logs, redeploy, restart, or remove deployments. Use for deployment lifecycle (remove, stop, redeploy, restart), deployment visibility (list, status, history), and troubleshooting (logs, errors, failures, crashes). NOT for deleting services - use railway-environment skill with isDeleted for that.

World-class data engineering skill for building scalable data pipelines, ETL/ELT systems, and data infrastructure. Expertise in Python, SQL, Spark, Airflow, dbt, Kafka, and modern data stack. Includes data modeling, pipeline orchestration, data quality, and DataOps. Use when designing data architectures, building data pipelines, optimizing data workflows, or implementing data governance.

Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.

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.

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows.

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.

World-class data science skill for statistical modeling, experimentation, causal inference, and advanced analytics. Expertise in Python (NumPy, Pandas, Scikit-learn), R, SQL, statistical methods, A/B testing, time series, and business intelligence. Includes experiment design, feature engineering, model evaluation, and stakeholder communication. Use when designing experiments, building predictive models, performing causal analysis, or driving data-driven decisions.

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

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: 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.

World-class computer vision skill for image/video processing, object detection, segmentation, and visual AI systems. Expertise in PyTorch, OpenCV, YOLO, SAM, diffusion models, and vision transformers. Includes 3D vision, video analysis, real-time processing, and production deployment. Use when building vision AI systems, implementing object detection, training custom vision models, or optimizing inference pipelines.

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, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.

Extract text and tables from PDF files, fill forms, merge documents. Use when working with PDF files or when the user mentions PDFs, forms, or document extraction.

This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.

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.

Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.

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.

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

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.

Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.

Generates creative domain name ideas for your project and checks availability across multiple TLDs (.com, .io, .dev, .ai, etc.). Saves hours of brainstorming and manual checking.

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.

Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.

Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.

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.

Perform code reviews following Sentry engineering practices. Use when reviewing pull requests, examining code changes, or providing feedback on code quality. Covers security, performance, testing, and design review.

Turn ideas into fully formed designs and specs through natural collaborative dialogue. Use when planning new features, designing architecture, or making significant changes to the codebase.

Manage issues, projects & team workflows in Linear. Use when the user wants to read, create or updates tickets in Linear.

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.

Implements the NOWAIT technique for efficient reasoning in R1-style LLMs. Use when optimizing inference of reasoning models (QwQ, DeepSeek-R1, Phi4-Reasoning, Qwen3, Kimi-VL, QvQ), reducing chain-of-thought token usage by 27-51% while preserving accuracy. Triggers on "optimize reasoning", "reduce thinking tokens", "efficient inference", "suppress reflection tokens", or when working with verbose CoT outputs.

Web accessibility specialist for WCAG compliance, ARIA implementation, and inclusive design. Use when auditing websites for accessibility issues, implementing WCAG 2.1 AA/AAA standards, testing with screen readers, or ensuring ADA compliance. Expert in semantic HTML, keyboard navigation, and assistive technology compatibility.

Query, stage, and apply configuration changes for Railway environments. Use for ANY variable or env var operations, service configuration (source, build settings, deploy settings), lifecycle (delete service), and applying changes. Prefer over railway-status skill for any configuration or variable queries.

Migrate prompts and code from Claude Sonnet 4.0, Sonnet 4.5, or Opus 4.1 to Opus 4.5. Use when the user wants to update their codebase, prompts, or API calls to use Opus 4.5. Handles model string updates and prompt adjustments for known Opus 4.5 behavioral differences. Does NOT migrate Haiku 4.5.

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.

Agile product ownership toolkit for Senior Product Owner including INVEST-compliant user story generation, sprint planning, backlog management, and velocity tracking. Use for story writing, sprint planning, stakeholder communication, and agile ceremonies.

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

Expert in integrating third-party APIs with proper authentication, error handling, rate limiting, and retry logic. Use when integrating REST APIs, GraphQL endpoints, webhooks, or external services. Specializes in OAuth flows, API key management, request/response transformation, and building robust API clients.