delphine-l-claude-global

Plugin delphine-l-claude-global from marketplace cascade-ai-ml-engineering in joshuarweaver/cascade-ai-ml-engineering. Commands read from the repo's manifest — 1 month ago.

Skills (33)

• 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.

• 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.

• documentation-organization

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

• 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.

• scientific-publication
• fundamentals
• phylogenetics
• visualization
• collaboration
• command-discipline
• documentation
• skill-management
• systematic-debugging
• token-efficiency
• verification-before-completion
• hackmd
• project-sharing
• bioservices
• gget
• gnomad
• automation
• tool-wrapping
• training-material
• workflow-development
• galaxy-workflow-viz
• workflow-maintenance-log
• conda-recipe
• data-backup
• folder-organization
• managing-environments
• obsidian
• genomeark-aws
• vgp-pipeline

Slash commands (76)

• /delphine-l-claude-global:galaxy-workflow-development:beautify_export_wkfl
• /delphine-l-claude-global:galaxy-workflow-development:iwc-workflow

  Prepare a Galaxy workflow file for IWC submission

• /delphine-l-claude-global:galaxy-workflow-development:prepare-for-iwc

  Prepare a Galaxy workflow for IWC submission (release version, cleanup, validation)

• /delphine-l-claude-global:galaxy-workflow-development:switch-workflow

  Switch to a VGP workflow directory and branch. Usage: /switch-workflow VGP8

• /delphine-l-claude-global:galaxy-workflow-development:update-export-workflow

  Update a Galaxy export workflow to match changes in its upstream analysis workflow

• /delphine-l-claude-global:global:backup

  Smart backup system with skill integration. Setup on first run, then daily/milestone backups with intelligent cleanup.

• /delphine-l-claude-global:global:backup:backup-script-template
• /delphine-l-claude-global:global:backup:execution-and-errors
• /delphine-l-claude-global:global:backup:setup-and-documentation
• /delphine-l-claude-global:global:challenge-mocks

  Challenge mock/patch usage in Python tests — identify tests that only test mocks and suggest real alternatives (DI, fakes, in-memory implementations)

• /delphine-l-claude-global:global:clean-after-claude

  Consolidate stray .claude/ subdirectories in a repo into a single clean setup at the git root - merges settings, flags promotable rules, preserves project-only skills/commands, consolidates project-config, and offers to clean up audit logs and stale state files

• /delphine-l-claude-global:global:cleanup-project

  End-of-project cleanup - removes working documentation and condenses verbose READMEs for files changed in current git branch

• /delphine-l-claude-global:global:clipdoc

  Copy the full contents of a file to the system clipboard

• /delphine-l-claude-global:global:clippath

  Copy the full path to a file to the system clipboard

• /delphine-l-claude-global:global:command-help

  Show help and documentation for Claude Code commands. Usage: /command-help [command-name]

• /delphine-l-claude-global:global:consolidate-notes

  Consolidate session notes, update project status, and archive processed notes with AI-powered analysis

• /delphine-l-claude-global:global:consolidate-notes:analysis-script
• /delphine-l-claude-global:global:consolidate-notes:redundancy-and-ai-analysis
• /delphine-l-claude-global:global:consolidate-notes:reference
• /delphine-l-claude-global:global:consolidate-notes:status-generation
• /delphine-l-claude-global:global:decompose-for-rebase

  Break up a messy commit into smaller, focused commits ready for interactive rebase

• /delphine-l-claude-global:global:deconflict

  Resolve git rebase/merge conflicts and explain the problems and solution

• /delphine-l-claude-global:global:dedup

  Analyze code for semantic duplication and generate a refactoring report with concrete before/after examples

• /delphine-l-claude-global:global:deprecate-file

  Deprecate files by moving them to deprecated/ folder, recursively handling dependencies, and updating MANIFESTs

• /delphine-l-claude-global:global:deprecate-file:dependency-detection
• /delphine-l-claude-global:global:deprecate-file:manifest-and-logging
• /delphine-l-claude-global:global:deprecate-file:safety-and-examples
• /delphine-l-claude-global:global:deprecate-file:setup-templates
• /delphine-l-claude-global:global:deprecate-file:usage-check-and-deprecation-tree
• /delphine-l-claude-global:global:design-and-plan

  Collaborative design and planning workflow for complex tasks. Brainstorm approaches, create a structured implementation plan, then execute. Use for new tools, analysis strategies, major refactors — anything that benefits from thinking before doing.

• /delphine-l-claude-global:global:generate-manifest

  Generate or update MANIFEST.md file inventories for project navigation and context efficiency

• /delphine-l-claude-global:global:list-skills

  List all available skills in $CLAUDE_METADATA with descriptions

• /delphine-l-claude-global:global:plan-clean

  Renumber phases/iterations/steps sequentially in a plan document and update all cross-references

• /delphine-l-claude-global:global:plan-debrief

  Compare an implemented plan against actual code — evaluate correctness, deviations, completeness, and propose prioritized next steps

• /delphine-l-claude-global:global:plan-integrate-questions

  Merge answered questions from a plan's unresolved section back into the main body of the plan

• /delphine-l-claude-global:global:plan-interview

  Deep interactive interview about a plan file — asks non-obvious questions about technical, implementation, UI/UX, and tradeoff decisions, then rewrites the plan with your answers incorporated

• /delphine-l-claude-global:global:plan-research-questions

  Launch parallel subagents to research each unresolved/open question in a plan file, then add findings back to the document

• /delphine-l-claude-global:global:plan-review

  Review an unimplemented plan for clarity, correctness, and feasibility. Optionally evaluate against a larger goal or parent plan

• /delphine-l-claude-global:global:plan-summary

  Summarize next steps from a plan, verify them against the repo, and prompt the user to choose what to work on

• /delphine-l-claude-global:global:read-manifest

  Smart session startup - read MANIFEST, select a task, load relevant context for current work

• /delphine-l-claude-global:global:resume-interrupted

  Recover from a crashed/interrupted session by processing the latest transcript backup into PROGRESS.md

• /delphine-l-claude-global:global:review-test

  Review test code for quality — challenge weak assertions, identify tests that should be eliminated, and suggest improvements for legibility

• /delphine-l-claude-global:global:safe-clear

  Save session notes to Obsidian, update skills with session knowledge, then clear context to continue working

• /delphine-l-claude-global:global:safe-clear:examples
• /delphine-l-claude-global:global:safe-clear:obsidian-integration
• /delphine-l-claude-global:global:safe-clear:reference
• /delphine-l-claude-global:global:safe-exit

  Safely end Claude Code session with backup and Obsidian session summary prompts

• /delphine-l-claude-global:global:safe-exit:examples
• /delphine-l-claude-global:global:safe-exit:obsidian-integration
• /delphine-l-claude-global:global:safe-exit:reference
• /delphine-l-claude-global:global:setup-environment

  Plan and set up the best Python environment type (venv or conda) for the current project

• /delphine-l-claude-global:global:setup-project

  Set up Claude Code skills for a new project

• /delphine-l-claude-global:global:share-project

  Prepare organized project package for sharing with collaborators, reviewers, or repositories. Creates clean copies at different levels (Summary/Reproducible/Full).

• /delphine-l-claude-global:global:share-project:abridging
• /delphine-l-claude-global:global:share-project:copy-and-clean
• /delphine-l-claude-global:global:share-project:file-selection
• /delphine-l-claude-global:global:share-project:manifest-parsing
• /delphine-l-claude-global:global:share-project:path-verification
• /delphine-l-claude-global:global:share-project:reference
• /delphine-l-claude-global:global:share-project:templates
• /delphine-l-claude-global:global:sync-skills

  Sync project with $CLAUDE_METADATA - detect new skills/commands to symlink

• /delphine-l-claude-global:global:sync-skills:detection-logic
• /delphine-l-claude-global:global:sync-skills:output-format
• /delphine-l-claude-global:global:sync-skills:special-cases
• /delphine-l-claude-global:global:update-manifest

  Quick-update existing MANIFEST.md files preserving user content - faster than full regeneration

• /delphine-l-claude-global:global:update-notebook

  Comprehensive Jupyter notebook maintenance - updates figures, verifies references, updates TOC, checks coherence

• /delphine-l-claude-global:global:update-notebook:execute-updates
• /delphine-l-claude-global:global:update-notebook:save-and-reference
• /delphine-l-claude-global:global:update-notebook:toc-and-legends
• /delphine-l-claude-global:global:update-notebook:validation-checks
• /delphine-l-claude-global:global:update-skills

  Review session and suggest skill updates to $CLAUDE_METADATA

• /delphine-l-claude-global:vgp-pipeline:check-status

  Check status of all VGP workflows

• /delphine-l-claude-global:vgp-pipeline:debug-failed

  Debug failed workflows for a species

• /delphine-l-claude-global:vgp-pipeline:optimize-token-usage

  Analyze and optimize Claude Code token usage

• /delphine-l-claude-global:vgp-pipeline:setup-cron

  Set up cron job for automated workflow monitoring

• /delphine-l-claude-global:vgp-pipeline:update-skills

  Review session and suggest skill updates

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