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Topic: codex

8,457 skills in this topic.

excel-analysis Analyze Excel spreadsheets, create pivot tables, generate charts, and perform data analysis. Use when analyzing Excel files, spreadsheets, tabular data, or .xlsx files.
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executing-plans Use when you have a written implementation plan to execute in a separate session with review checkpoints
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find-bugs 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.
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finishing-a-development-branch Use when implementation is complete, all tests pass, and you need to decide how to integrate the work - guides completion of development work by presenting structured options for merge, PR, or cleanup
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gdpr-dsgvo-expert Senior GDPR/DSGVO expert and internal/external auditor for data protection compliance. Provides EU GDPR and German DSGVO expertise, privacy impact assessments, data protection auditing, and compliance verification. Use for GDPR compliance assessments, privacy audits, data protection planning, and regulatory compliance verification.
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gene-database Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
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generate-image Generate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that isn't a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.
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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.
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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.
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gget CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.
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gh-fix-ci 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.
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gtars High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
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hypogenic Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.
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internal-comms A set of resources to help me write all kinds of internal communications, using the formats that my company likes to use. Claude should use this skill whenever asked to write some sort of internal communications (status reports, leadership updates, 3P updates, company newsletters, FAQs, incident reports, project updates, etc.).
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invoice-organizer 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.
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isms-audit-expert Senior ISMS Audit Expert for internal and external information security management system auditing. Provides ISO 27001 audit expertise, security audit program management, security control assessment, and compliance verification. Use for ISMS internal auditing, external audit preparation, security control testing, and ISO 27001 certification support.
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iterate-pr 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.
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labarchive-integration Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
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lamindb 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.
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lead-research-assistant Identifies high-quality leads for your product or service by analyzing your business, searching for target companies, and providing actionable contact strategies. Perfect for sales, business development, and marketing professionals.
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linear Manage issues, projects & team workflows in Linear. Use when the user wants to read, create or updates tickets in Linear.
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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.).
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matchms Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
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mcp-builder 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 external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
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