delphine-l/claude_global
32 skills3.7k installs544 starsGitHub
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npx skills add https://github.com/delphine-l/claude_globalSkills in this repo
1Token EfficiencyToken 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 The token-efficiency skill documents workflows and patterns from the repository SKILL md name token-efficiency description 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 version 1 5 0 allowed-tools Read Grep Glob Bash Token Efficiency Expert This skill provides token optimization strategies for cost-effective Claude Code usage across all projects These guidelines help minimize token consumption while maintaining high-quality assistance Core Principle ALWAYS follow these optimization guidelines by default unless the user explicitly requests verbose output or full file contents Default assumption Users prefer efficient cost-effective assistance Model Selecti.1.9kinstalls2Bioinformatics Fundamentalsbioinformatics-fundamentals is a domain skill from delphine-l/claude_global that steers agents toward biologically and statistically sound decisions when scoping bioinformatics software. It applies when designing genomic pipelines, proteomic workflows, or sequence-analysis features where incorrect biological assumptions or weak statistical framing create costly rework. The skill helps developers check whether proposed data models, normalization steps, and analysis methods align with established bioinformatics practice before writing pipeline code or lab-facing tools. Reach for bioinformatics-fundamentals at the design and scoping stage—not for generic Python debugging—when features touch FASTA/FASTQ processing, alignment, variant calling, expression analysis, or multi-omics integration. It pairs with implementation skills by front-loading domain correctness.408installs3Folder OrganizationDefines how to organize Claude and software project directories for long-term maintainability. Covers root layout, feature modules, shared assets, configuration zones, and documentation placement so humans and coding agents find files quickly and avoid duplicate or ambiguous paths.143installs4Bioinformatics Visualizationbioinformatics-visualization is a Claude Code skill for ai & agent building. It helps solo builders move faster with AI-assisted development.107installs5Obsidianobsidian is a Claude Code skill for ai & agent building. It helps solo builders move faster with AI-assisted development.93installs6Jupyter Notebook AnalysisGuides creation of comprehensive multi-cell Jupyter analyses with statistical testing, outlier strategies, and figure generation. A developer uses it when building rigorous notebook data analyses or figures to share with AI tools.79installs7Managing EnvironmentsEnforces checking and confirming the active Python environment before any package installation. A developer uses it to avoid installing dependencies into the wrong venv or conda environment.73installs8Claude CollaborationDocuments best practices for using Claude Code in team environments, treating skills as living documentation kept in a centralized repository and symlinked into projects. A developer uses it to standardize skill management, knowledge capture, and version control across a team.63installs9Claude Skill ManagementAn expert guide for managing Claude Code global skills and commands using a centralized $CLAUDE_METADATA repository pattern. A developer uses it when creating new skills, symlinking them into projects, syncing updates, organizing the repo, or troubleshooting skill discovery and activation.62installs10Conda RecipeA specialized assistant for building and testing conda/bioconda recipes, covering recipe creation, linting, dependency management, and build debugging. A developer uses it when packaging software for conda following bioconda best practices, including meta.yaml structure, sha256 checksums, and local builds.59installs11Project Sharingproject-sharing is a Claude Code skill for ai & agent building. It helps solo builders move faster with AI-assisted development.45installs12Galaxy AutomationProvides expert patterns for automating Galaxy bioinformatics workflows using BioBlend and Planemo. A developer uses it to invoke workflows, poll status, and manage histories and datasets programmatically.44installs13Scientific Publicationscientific-publication is a Claude Code skill for ai & agent building. It helps solo builders move faster with AI-assisted development.43installs14Galaxy Tool WrappingExpert guidance for creating, testing, and debugging Galaxy tool XML wrappers. A developer uses it when converting command-line tools into Galaxy tools or preparing them for Tool Shed submission.42installs15Galaxy Workflow DevelopmentProvides IWC-standard guidance for developing and testing Galaxy .ga workflow JSON files. A developer uses it to author or validate workflows with correct metadata and structure.42installs16Data VisualizationGuides creation of clear, accurate scientific visualizations and avoiding distortions like log-scale and coordinate-transform bugs. A developer uses it when generating publication figures or debugging misleading plots.36installs17Data Analysis PatternsProvides decision patterns for data aggregation, recalculation, and category changes in scientific analyses. A developer uses it when accuracy in publication-grade analysis pipelines depends on whether to recompute or reuse aggregated data.35installs18Data BackupRuns a smart backup workflow that detects notebooks, data files, and docs and applies cleanup before archiving, with CHANGELOG tracking. A developer uses it on long-running data projects to avoid losing work and to track data provenance.32installs19Verification Before CompletionRequires running a proof command and reading its full output before claiming tests pass or a bug is fixed. A developer uses it as a gate to avoid premature or unverified success claims.30installs20DocumentationDescribes how to write incremental summary documents, fix reports, and audit trails during coding sessions. A developer uses it to keep a clear record of what was changed and why across multiple fixes.29installs21Systematic Debuggingsystematic-debugging is a Claude Code skill for debugging. It helps solo builders move faster with AI-assisted development.29installs22GgetProvides unified CLI and Python access to over 20 genomic databases via gget for quick lookups and exploration. A developer uses it for interactive gene lookups, sequence retrieval, and enrichment analysis.28installs23HackmdCovers HackMD-compatible markdown authoring, slide mode, and embedded SVG best practices. A developer uses it when writing collaborative docs or slide decks on HackMD.28installs24BioservicesProvides a Python interface to roughly 40 bioinformatics web services, handling REST and SOAP transparently for cross-database analysis. A developer uses it for multi-service workflows like UniProt/KEGG/ChEMBL queries, cross-database ID mapping, pathway analysis, and protein-protein interaction lookups.27installs25Documentation OrganizationStructures project documentation so working files and shareable outputs stay separate and easy to package. A developer uses it to keep research project docs clean and ready for collaboration or sharing.27installs26Phylogeneticsphylogenetics is a Claude Code skill for ai & agent building. It helps solo builders move faster with AI-assisted development.26installs27Gnomad DatabaseGuides querying gnomAD for human genetic variation data via its GraphQL API for variant interpretation. A developer uses it to assess variant pathogenicity, rarity, and gene constraint.25installs28Galaxy Training MaterialCovers the custom GTN markdown syntax and structure for authoring Galaxy Training Network tutorials. A developer uses it when writing or fixing tutorial content in the galaxyproject/training-material repository.22installs29Genomeark AwsGuides access to the public GenomeArk S3 bucket for VGP assemblies and quality-control data using no-sign-request AWS CLI. A developer uses it to build pipelines that fetch genome assemblies and QC metrics.22installs30Vgp PipelineCovers VGP assembly workflow selection, execution patterns, and quality-control checkpoints on Galaxy. A developer uses it to run vertebrate genome assemblies and avoid pitfalls like full user quotas.22installs31Command DisciplineA behavior rule instructing an agent to run shell commands directly, without decorative echo headers, echo-then-command chains, or trailing status echoes. A developer or agent uses it to keep Bash invocations clean and to avoid breaking permission-rule auto-approval that matches on the first command segment.13installs32Workflow Maintenance LogPrescribes one Obsidian log note per workflow version-bump recording changes, test edits, and planemo history. A developer uses it when maintaining IWC/Galaxy workflows to keep test runs auditable and avoid unnecessary full re-runs.12installs