delphine-l
- 32 skills
- 0 followers
- 1 week ago last updated
- ▌ Gget · delphine-l bundleFast 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.
- ▌ Gnomad Database · delphine-l bundleQuery 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.
- ▌ Vgp Pipeline · delphine-l bundleVGP assembly pipeline - Galaxy workflow selection, execution patterns, QC checkpoints, and batch orchestration
- ▌ Galaxy Automation · delphine-l bundleBioBlend 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.
- ▌ Genomeark AWS · delphine-l bundleAccess and navigate GenomeArk AWS S3 bucket - VGP assemblies, QC data, and species directory structure
- ▌ Hackmd · delphine-lHackMD collaborative markdown - slide presentations, embedded SVG diagrams, and real-time editing best practices
- ▌ Galaxy Tool Wrapping · delphine-l bundleExpert in Galaxy tool wrapper development, XML schemas, Planemo testing, and best practices for creating Galaxy tools
- ▌ Bioservices · delphine-l bundleUnified 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.
- ▌ Conda Recipe · delphine-lExpert in building and testing conda/bioconda recipes, including recipe creation, linting, dependency management, and debugging common build errors
- ▌ Galaxy Training Material · delphine-l bundleExpert 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.
- ▌ Jupyter Notebook Analysis · delphine-l bundleBest practices for creating comprehensive Jupyter notebook data analyses with statistical rigor, outlier handling, and publication-quality visualizations. Includes Claude API image size helpers.
- ▌ Claude Collaboration · delphine-l bundleBest practices for using Claude Code in team environments. Covers skill management, knowledge capture, version control, and collaborative workflows.
- ▌ Documentation · delphine-lBest practices for session documentation - incremental summaries, fix reports, and audit trails
- ▌ Data Visualization · delphine-l bundleBest 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.
- ▌ Bioinformatics Fundamentals · delphine-l bundleCore 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.
- ▌ Galaxy Workflow Development · delphine-l bundleExpert in Galaxy workflow development, testing, and IWC best practices. Create, validate, and optimize .ga workflows following Intergalactic Workflow Commission standards.
- ▌ Obsidian · delphine-l bundleIntegration 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+).
- ▌ Phylogenetics · delphine-lPhylogenetic tree analysis, visualization, annotation management, and iTOL troubleshooting
- ▌ Bioinformatics Visualization · delphine-lPublication-quality bioinformatics figures - phylogenetic trees, genome browsers, iTOL datasets, and data presentation
- ▌ Claude Skill Management · delphine-l bundleExpert 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.
- ▌ Token Efficiency · delphine-l bundleToken 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.
- ▌ Command Discipline · delphine-lRun 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.
- ▌ Data Backup · delphine-l bundleSmart 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.
- ▌ Data Analysis Patterns · delphine-l bundleBest 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.
- ▌ Scientific Publication · delphine-l bundleBest practices for iterative refinement of publication-quality scientific figures. Covers systematic improvement workflows, layout optimization, and ensuring all figure elements are publication-ready.
- ▌ Workflow Maintenance Log · delphine-lMaintain 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 any session that edits `.ga`, edits `-tests.yml`, runs `planemo test`/`planemo workflow_test_on_invocation`, or prepares an IWC PR.
- ▌ Systematic Debugging · delphine-l bundleStructured 4-phase debugging methodology. Use when encountering any bug, test failure, unexpected behavior, or pipeline error — before proposing fixes. Enforces root cause investigation first.
- ▌ Documentation Organization · delphine-l bundleOrganize research project documentation - structure working files, prepare sharing packages, maintain clean project layout
- ▌ Folder Organization · delphine-l bundleBest practices for organizing project folders, file naming conventions, and directory structure standards for research and development projects
- ▌ Managing Environments · delphine-l bundleBest practices for managing development environments including Python venv and conda. Always check environment status before installations and confirm with user before proceeding.
- ▌ Verification Before Completion · delphine-lEnforces 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.
- ▌ Galaxy Workflow Viz · delphine-l bundleGenerate Galaxy-branded workflow visualization SVGs for IWC workflows. Creates static diagrams matching Galaxy's workflow editor style with bezier connections, node cards, and proper terminal positioning. Use when creating visual diagrams for workflows in this repository.