Skill Claude CodeCodex
Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for [intervention]", or when developing FDA submission documentation for…
Skill Claude CodeCodex
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
Skill Claude CodeCodex
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis…
Skill Claude CodeCodex
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate…
Skill Claude CodeCodex
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics…
Skill Claude CodeCodex
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
Skill Claude CodeCodex
Customize or personalize a Claude Code plugin for a specific organization's tools and workflows. Use when users want to customize a plugin, replace tool placeholders, or configure MCP servers for a plugin. This skill requires Cowork mode with mounted plugin directories and will not work in remote or standard CLI…
Skill Claude CodeCodex
Research customer questions by searching across documentation, knowledge bases, and connected sources, then synthesize a confidence-scored answer. Use when a customer asks a question you need to investigate, when building background on a customer situation, or when you need account context.
Skill Claude CodeCodex
Structure and package support escalations for engineering, product, or leadership with full context, reproduction steps, and business impact. Use when an issue needs to go beyond support, when writing an escalation brief, or when assessing whether an issue warrants escalation.
Skill Claude CodeCodex
Write and maintain knowledge base articles from resolved support issues. Use when a ticket has been resolved and the solution should be documented, when updating existing KB articles, or when creating how-to guides, troubleshooting docs, or FAQ entries.
Skill Claude CodeCodex
Triage incoming support tickets by categorizing issues, assigning priority (P1-P4), and recommending routing. Use when a new ticket or customer issue comes in, when assessing severity, or when deciding which team should handle an issue.
Skill Claude CodeCodex
Generate or improve a company-specific data analysis skill by extracting tribal knowledge from analysts. BOOTSTRAP MODE - Triggers: "Create a data context skill", "Set up data analysis for our warehouse", "Help me create a skill for our database", "Generate a data skill for [company]" → Discovers schemas, asks key…
Skill Claude CodeCodex
Profile and explore datasets to understand their shape, quality, and patterns before analysis. Use when encountering a new dataset, assessing data quality, discovering column distributions, identifying nulls and outliers, or deciding which dimensions to analyze.
Skill Claude CodeCodex
QA an analysis before sharing with stakeholders — methodology checks, accuracy verification, and bias detection. Use when reviewing an analysis for errors, checking for survivorship bias, validating aggregation logic, or preparing documentation for reproducibility.
Skill Claude CodeCodex
Create effective data visualizations with Python (matplotlib, seaborn, plotly). Use when building charts, choosing the right chart type for a dataset, creating publication-quality figures, or applying design principles like accessibility and color theory.
Skill Claude CodeCodex
Build self-contained interactive HTML dashboards with Chart.js, dropdown filters, and professional styling. Use when creating dashboards, building interactive reports, or generating shareable HTML files with charts and filters that work without a server.
Skill Claude CodeCodex
Write correct, performant SQL across all major data warehouse dialects (Snowflake, BigQuery, Databricks, PostgreSQL, etc.). Use when writing queries, optimizing slow SQL, translating between dialects, or building complex analytical queries with CTEs, window functions, or aggregations.
Skill Claude CodeCodex
Apply statistical methods including descriptive stats, trend analysis, outlier detection, and hypothesis testing. Use when analyzing distributions, testing for significance, detecting anomalies, computing correlations, or interpreting statistical results.
Skill Claude CodeCodex
Combines search results from multiple sources into coherent, deduplicated answers with source attribution. Handles confidence scoring based on freshness and authority, and summarizes large result sets effectively.
Skill Claude CodeCodex
Query decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries into source-specific syntax, ranks results by relevance, and handles ambiguity and fallback strategies.
Skill Claude CodeCodex
Manages connected MCP sources for enterprise search. Detects available sources, guides users to connect new ones, handles source priority ordering, and manages rate limiting awareness.
Skill Claude CodeCodex
Support SOX 404 compliance with control testing methodology, sample selection, and documentation standards. Use when generating testing workpapers, selecting audit samples, classifying control deficiencies, or preparing for internal or external audits.
Skill Claude CodeCodex
Manage the month-end close process with task sequencing, dependencies, and status tracking. Use when planning the close calendar, tracking close progress, identifying blockers, or sequencing close activities by day.
Skill Claude CodeCodex
Generate income statements, balance sheets, and cash flow statements with GAAP presentation and period-over-period comparison. Use when preparing financial statements, running flux analysis, or creating P&L reports with variance commentary.