claude_global

In the author's own words, from each skill's SKILL.md — showing the first 30 of 33 files.

• data-analysis-patterns

  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.

  skills/analysis/data-analysis-patterns/SKILL.md on GitHub (opens in a new tab)

• data-visualization

  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.

  skills/analysis/data-visualization/SKILL.md on GitHub (opens in a new tab)

• documentation-organization

  Organize research project documentation - structure working files, prepare sharing packages, maintain clean project layout

  skills/analysis/documentation-organization/SKILL.md on GitHub (opens in a new tab)

• jupyter-notebook-analysis

  Best practices for creating comprehensive Jupyter notebook data analyses with statistical rigor, outlier handling, and publication-quality visualizations. Includes Claude API image size helpers.

  skills/analysis/jupyter-notebook/SKILL.md on GitHub (opens in a new tab)

• scientific-publication

  Best practices for iterative refinement of publication-quality scientific figures. Covers systematic improvement workflows, layout optimization, and ensuring all figure elements are publication-ready.

  skills/analysis/scientific-publication/SKILL.md on GitHub (opens in a new tab)

• bioinformatics-fundamentals

  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.

  skills/bioinformatics/fundamentals/SKILL.md on GitHub (opens in a new tab)

• phylogenetics

  Phylogenetic tree analysis, visualization, annotation management, and iTOL troubleshooting

  skills/bioinformatics/phylogenetics/SKILL.md on GitHub (opens in a new tab)

• bioinformatics-visualization

  Publication-quality bioinformatics figures - phylogenetic trees, genome browsers, iTOL datasets, and data presentation

  skills/bioinformatics/visualization/SKILL.md on GitHub (opens in a new tab)

• claude-collaboration

  Best practices for using Claude Code in team environments. Covers skill management, knowledge capture, version control, and collaborative workflows.

  skills/claude-meta/collaboration/SKILL.md on GitHub (opens in a new tab)

• command-discipline

  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.

  skills/claude-meta/command-discipline/SKILL.md on GitHub (opens in a new tab)

• documentation

  Best practices for session documentation - incremental summaries, fix reports, and audit trails

  skills/claude-meta/documentation/SKILL.md on GitHub (opens in a new tab)

• claude-skill-management

  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.

  skills/claude-meta/skill-management/SKILL.md on GitHub (opens in a new tab)

• systematic-debugging

  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.

  skills/claude-meta/systematic-debugging/SKILL.md on GitHub (opens in a new tab)

• token-efficiency

  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.

  skills/claude-meta/token-efficiency/SKILL.md on GitHub (opens in a new tab)

• verification-before-completion

  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.

  skills/claude-meta/verification-before-completion/SKILL.md on GitHub (opens in a new tab)

• hackmd

  HackMD collaborative markdown - slide presentations, embedded SVG diagrams, and real-time editing best practices

  skills/collaboration/hackmd/SKILL.md on GitHub (opens in a new tab)

• project-sharing

  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.

  skills/collaboration/project-sharing/SKILL.md on GitHub (opens in a new tab)

• bioservices

  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.

  skills/databases/bioservices/SKILL.md on GitHub (opens in a new tab)

• gget

  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.

  skills/databases/gget/SKILL.md on GitHub (opens in a new tab)

• gnomad-database

  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.

  skills/databases/gnomad/SKILL.md on GitHub (opens in a new tab)

• galaxy-automation

  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.

  skills/galaxy/automation/SKILL.md on GitHub (opens in a new tab)

• galaxy-tool-wrapping

  Expert in Galaxy tool wrapper development, XML schemas, Planemo testing, and best practices for creating Galaxy tools

  skills/galaxy/tool-wrapping/SKILL.md on GitHub (opens in a new tab)

• galaxy-training-material

  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.

  skills/galaxy/training-material/SKILL.md on GitHub (opens in a new tab)

• galaxy-workflow-development

  Expert in Galaxy workflow development, testing, and IWC best practices. Create, validate, and optimize .ga workflows following Intergalactic Workflow Commission standards.

  skills/galaxy/workflow-development/SKILL.md on GitHub (opens in a new tab)

• workflow-maintenance-log

  Maintain per-workflow developer logs in Obsidian when working on Galaxy workflows. Use whenever creating, version-bumping, fixing, or updating an IWC/Galaxy `.ga` workflow or its `-tests.yml`. Logs detailed changes, test YAML edits, and `planemo` invocation history so the correct planemo command (full `planemo test` vs fast `workflow_test_on_invocation`) is obvious without guessing. Triggers on a…

  skills/galaxy/workflow-maintenance-log/SKILL.md on GitHub (opens in a new tab)

• conda-recipe

  Expert in building and testing conda/bioconda recipes, including recipe creation, linting, dependency management, and debugging common build errors

  skills/packaging/conda-recipe/SKILL.md on GitHub (opens in a new tab)

• data-backup

  Smart automated backup system with skill integration. Detects project type (notebooks, data files, HackMD docs) and applies appropriate cleanup before backup. Rolling daily backups, compressed milestones, and CHANGELOG tracking.

  skills/project-management/data-backup/SKILL.md on GitHub (opens in a new tab)

• folder-organization

  Best practices for organizing project folders, file naming conventions, and directory structure standards for research and development projects

  skills/project-management/folder-organization/SKILL.md on GitHub (opens in a new tab)

• managing-environments

  Best practices for managing development environments including Python venv and conda. Always check environment status before installations and confirm with user before proceeding.

  skills/project-management/managing-environments/SKILL.md on GitHub (opens in a new tab)

• obsidian

  Integration with Obsidian vault for managing notes, tasks, and knowledge when working with Claude. Supports adding notes, creating tasks, and organizing project documentation. Updated with 2025-2026 best practices including MOCs, properties, practical organization patterns, and Obsidian CLI (1.12+).

  skills/project-management/obsidian/SKILL.md on GitHub (opens in a new tab)

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