Skill Claude CodeCodex
Best practices for data aggregation, recalculation, and category management in scientific analyses. Covers when to recalculate vs reuse aggregated data, handling category changes, and ensuring analytical accuracy.
Skill Claude CodeCodex
Best practices for creating clear, accurate scientific visualizations with matplotlib, seaborn, and other Python plotting libraries. Covers common pitfalls, optimization techniques, publication-quality figure generation, and Claude API image size constraints.
Skill Claude CodeCodex
Organize research project documentation - structure working files, prepare sharing packages, maintain clean project layout.
Skill Claude CodeCodex
Best practices for creating comprehensive Jupyter notebook data analyses with statistical rigor, outlier handling, and publication-quality visualizations. Includes Claude API image size helpers.
Skill Claude CodeCodex
Best practices for iterative refinement of publication-quality scientific figures. Covers systematic improvement workflows, layout optimization, and ensuring all figure elements are publication-ready.
Skill Claude CodeCodex
Core bioinformatics concepts including SAM/BAM format, AGP genome assembly format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, pairing issues, and AGP coordinate validation.
Skill Claude CodeCodex
Phylogenetic tree analysis, visualization, annotation management, and iTOL troubleshooting.
Skill Claude CodeCodex
Publication-quality bioinformatics figures - phylogenetic trees, genome browsers, iTOL datasets, and data presentation.
Skill Claude CodeCodex
Best practices for using Claude Code in team environments. Covers skill management, knowledge capture, version control, and collaborative workflows.
Skill Claude CodeCodex
Run shell commands bare — no decorative echo headers ("=== X ==="), no echo-then-cmd chains, no trailing "echo done". Use the Bash tool's description field for any narration. Triggers any time you're about to issue a Bash command.
Skill Claude CodeCodex
Best practices for session documentation - incremental summaries, fix reports, and audit trails.
Skill Claude CodeCodex
Expert guide for managing Claude Code global skills and commands. Use when creating new skills, symlinking to projects, updating existing skills, or organizing the centralized skill repository.
Skill Claude CodeCodex
Structured 4-phase debugging methodology. Use when encountering any bug, test failure, unexpected behavior, or pipeline error — before proposing fixes. Enforces root cause investigation first.
Skill Claude CodeCodex
Token optimization best practices for cost-effective Claude Code usage. Automatically applies efficient file reading, command execution, and output handling strategies. Includes model selection guidance (Opus for learning, Sonnet for development/debugging). Prefers bash commands over reading files.
Skill Claude CodeCodex
Enforces evidence-based completion claims. Use before claiming work is done, tests pass, or bugs are fixed. Requires running verification commands and confirming output before any success claims.
Skill Claude CodeCodex
HackMD collaborative markdown - slide presentations, embedded SVG diagrams, and real-time editing best practices.
Skill Claude CodeCodex
Prepare organized packages of project files for sharing at different levels - from summary PDFs to fully reproducible archives. Creates copies with cleaned notebooks, documentation, and appropriate file selection. After creating sharing package, all work continues in the main project directory.
Skill Claude CodeCodex
Unified Python interface to 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome, PSICQUIC). Best for cross-database analysis, ID mapping, and multi-service workflows. For quick single-database lookups use gget.
Skill Claude CodeCodex
Fast CLI/Python queries to 20+ bioinformatics databases. Gene info, BLAST, AlphaFold structures, enrichment analysis, single-cell data, disease associations. Best for interactive exploration and quick lookups. For batch/multi-database Python workflows use bioservices.
Skill Claude CodeCodex
Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance via GraphQL API. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes.
Skill Claude CodeCodex
BioBlend and Planemo expertise for Galaxy workflow automation. Galaxy API usage, workflow invocation, status checking, error handling, batch processing, and dataset management. Essential for any Galaxy automation project.
Skill Claude CodeCodex
Expert in Galaxy tool wrapper development, XML schemas, Planemo testing, and best practices for creating Galaxy tools.
Skill Claude CodeCodex
Expert in Galaxy Training Network (GTN) tutorial development. GTN markdown syntax, special boxes, tool references, snippets, YAML front matter, and best practices for writing and updating training materials in the galaxyproject/training-material repository.
Skill Claude CodeCodex
Expert in Galaxy workflow development, testing, and IWC best practices. Create, validate, and optimize .ga workflows following Intergalactic Workflow Commission standards.