Tools

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

Automatically organizes invoices and receipts for tax preparation by reading messy files, extracting key information, renaming them consistently, and sorting them into logical folders. Turns hours of manual bookkeeping into minutes of automated organization.

Comprehensive backend development skill for building scalable backend systems using NodeJS, Express, Go, Python, Postgres, GraphQL, REST APIs. Includes API scaffolding, database optimization, security implementation, and performance tuning. Use when designing APIs, optimizing database queries, implementing business logic, handling authentication/authorization, or reviewing backend code.

Inspect GitHub PR checks with gh, pull failing GitHub Actions logs, summarize failure context, then create a fix plan and implement after user approval. Use when a user asks to debug or fix failing PR CI/CD checks on GitHub Actions and wants a plan + code changes; for external checks (e.g., Buildkite), only report the details URL and mark them out of scope.

Generate descriptive commit messages by analyzing git diffs. Use when the user asks for help writing commit messages or reviewing staged changes.

Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.

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.

Production-ready PDF processing with forms, tables, OCR, validation, and batch operations. Use when working with complex PDF workflows in production environments, processing large volumes of PDFs, or requiring robust error handling and validation.

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.

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.

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.

Manage and trigger pre-built Zapier workflows and MCP tool orchestration. Use when user mentions workflows, Zaps, automations, daily digest, research, search, lead tracking, expenses, or asks to "run" any process. Also handles Perplexity-based research and Google Sheets data tracking.

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.

Comprehensive frontend development skill for building modern, performant web applications using ReactJS, NextJS, TypeScript, Tailwind CSS. Includes component scaffolding, performance optimization, bundle analysis, and UI best practices. Use when developing frontend features, optimizing performance, implementing UI/UX designs, managing state, or reviewing frontend code.

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

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

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.

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.

Automatically creates user-facing changelogs from git commits by analyzing commit history, categorizing changes, and transforming technical commits into clear, customer-friendly release notes. Turns hours of manual changelog writing into minutes of automated generation.

Comprehensive SecOps skill for application security, vulnerability management, compliance, and secure development practices. Includes security scanning, vulnerability assessment, compliance checking, and security automation. Use when implementing security controls, conducting security audits, responding to vulnerabilities, or ensuring compliance requirements.