delphine-l/claude_global

5772

token-efficiency Token optimization best practices for cost-effective Claude Code usage. Automatically applies efficient file reading,…

delphine-l/claude_global

2.2K

2

bioinformatics-fundamentals Core bioinformatics concepts including SAM/BAM format, AGP genome assembly format, sequencing technologies (Hi-C, HiF…

delphine-l/claude_global

430

3

folder-organization Best practices for organizing project folders, file naming conventions, and directory structure standards for researc…

delphine-l/claude_global

150

4

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

delphine-l/claude_global

119

5

obsidian Integration with Obsidian vault for managing notes, tasks, and knowledge when working with Claude. Supports adding no…

delphine-l/claude_global

99

6

jupyter-notebook-analysis Best practices for creating comprehensive Jupyter notebook data analyses with statistical rigor, outlier handling, an…

delphine-l/claude_global

83

7

managing-environments Best practices for managing development environments including Python venv and conda. Always check environment status…

delphine-l/claude_global

79

8

claude-collaboration Best practices for using Claude Code in team environments. Covers skill management, knowledge capture, version contro…

delphine-l/claude_global

68

9

claude-skill-management Expert guide for managing Claude Code global skills and commands. Use when creating new skills, symlinking to project…

delphine-l/claude_global

66

10

conda-recipe Expert in building and testing conda/bioconda recipes, including recipe creation, linting, dependency management, and…

delphine-l/claude_global

63

11

galaxy-automation BioBlend and Planemo expertise for Galaxy workflow automation. Galaxy API usage, workflow invocation, status checking…

delphine-l/claude_global

50

12

project-sharing Prepare organized packages of project files for sharing at different levels - from summary PDFs to fully reproducible…

delphine-l/claude_global

50

13

scientific-publication Best practices for iterative refinement of publication-quality scientific figures. Covers systematic improvement work…

delphine-l/claude_global

49

14

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

delphine-l/claude_global

47

15

galaxy-workflow-development Expert in Galaxy workflow development, testing, and IWC best practices. Create, validate, and optimize .ga workflows …

delphine-l/claude_global

47

16

data-analysis-patterns Best practices for data aggregation, recalculation, and category management in scientific analyses. Covers when to re…

delphine-l/claude_global

40

17

data-visualization Best practices for creating clear, accurate scientific visualizations with matplotlib, seaborn, and other Python plot…

delphine-l/claude_global

40

18

data-backup Smart automated backup system with skill integration. Detects project type (notebooks, data files, HackMD docs) and a…

delphine-l/claude_global

37

19

verification-before-completion Enforces evidence-based completion claims. Use before claiming work is done, tests pass, or bugs are fixed. Requires …

delphine-l/claude_global

35

20

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

delphine-l/claude_global

34

21

bioservices Unified Python interface to 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome, PSICQUIC). Best for cross-d…

delphine-l/claude_global

33

22

documentation-organization Organize research project documentation - structure working files, prepare sharing packages, maintain clean project l…

delphine-l/claude_global

33

23

gget Fast CLI/Python queries to 20+ bioinformatics databases. Gene info, BLAST, AlphaFold structures, enrichment analysis,…

delphine-l/claude_global

33

24

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

delphine-l/claude_global

33

25

systematic-debugging Structured 4-phase debugging methodology. Use when encountering any bug, test failure, unexpected behavior, or pipeli…

delphine-l/claude_global

33

26

gnomad-database Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF),…

delphine-l/claude_global

31

27

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

delphine-l/claude_global

31

28

galaxy-training-material Expert in Galaxy Training Network (GTN) tutorial development. GTN markdown syntax, special boxes, tool references, sn…

delphine-l/claude_global

27

29

genomeark-aws Access and navigate GenomeArk AWS S3 bucket - VGP assemblies, QC data, and species directory structure

delphine-l/claude_global

27

30

vgp-pipeline VGP assembly pipeline - Galaxy workflow selection, execution patterns, QC checkpoints, and batch orchestration

delphine-l/claude_global

27

31

command-discipline Run shell commands bare — no decorative echo headers ("=== X ==="), no echo-then-cmd chains, no trailing "echo done".…

delphine-l/claude_global

19

32

workflow-maintenance-log Maintain per-workflow developer logs in Obsidian when working on Galaxy workflows. Use whenever creating, version-bum…

delphine-l/claude_global

17