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Setup & scaffolding

5,913 rows, by stacks then stars

1,967 of these skill files have been read, by 1,553 distinct authors, and what they tell an agent counted. What Setup & scaffolding authors agree on, and what they forbid

  • Dataset code link extraction starter

    ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/dataset-code-link-extraction-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Figure table caption extraction starter

    ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/figure-table-caption-extraction-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Openalex citation chain starter

    ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/openalex-citation-chain-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Protocol and workflow extraction starter

    ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/protocol-and-workflow-extraction-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Reproducibility cue extraction starter

    ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/reproducibility-cue-extraction-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Scientific summarization starter

    ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/scientific-summarization-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Semantic scholar paper triage starter

    ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/semantic-scholar-paper-triage-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Semantic scholar review paper mining starter

    ma-compbio-lab/SkillFoundry/skills/scientific-knowledge/semantic-scholar-review-paper-mining-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Active learning starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/active-learning-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Arviz posterior diagnostics starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/arviz-posterior-diagnostics-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Clustering starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/clustering-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Dowhy average treatment effect starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/dowhy-average-treatment-effect-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Foundation models for biology chemistry science starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/foundation-models-for-biology-chemistry-science-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Multimodal fusion starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/multimodal-fusion-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Optuna bayesian optimization starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/optuna-bayesian-optimization-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Pydoe3 experimental design starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/pydoe3-experimental-design-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Pymc bayesian linear regression starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/pymc-bayesian-linear-regression-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Representation learning starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/representation-learning-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Scipy statistical testing starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/scipy-statistical-testing-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Simulation based inference starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/simulation-based-inference-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Umap dimensionality reduction starter

    ma-compbio-lab/SkillFoundry/skills/statistical-and-machine-learning-foundations-for-science/umap-dimensionality-reduction-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Binding site analysis starter

    ma-compbio-lab/SkillFoundry/skills/structural-biology/binding-site-analysis-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Fold comparison starter

    ma-compbio-lab/SkillFoundry/skills/structural-biology/fold-comparison-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Protein complex metadata starter

    ma-compbio-lab/SkillFoundry/skills/structural-biology/protein-complex-metadata-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Sequence structure alignment starter

    ma-compbio-lab/SkillFoundry/skills/structural-biology/sequence-structure-alignment-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Structure parsing and cleanup starter

    ma-compbio-lab/SkillFoundry/skills/structural-biology/structure-parsing-and-cleanup-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Structure to sequence cross linking starter

    ma-compbio-lab/SkillFoundry/skills/structural-biology/structure-to-sequence-cross-linking-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Visualization starter

    ma-compbio-lab/SkillFoundry/skills/structural-biology/visualization-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Causal network analysis starter

    ma-compbio-lab/SkillFoundry/skills/systems-biology/causal-network-analysis-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Networkx graph construction starter

    ma-compbio-lab/SkillFoundry/skills/systems-biology/networkx-graph-construction-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Networkx network propagation starter

    ma-compbio-lab/SkillFoundry/skills/systems-biology/networkx-network-propagation-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Reactome pathway analysis starter

    ma-compbio-lab/SkillFoundry/skills/systems-biology/reactome-pathway-analysis-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Reactome pathway hierarchy walk starter

    ma-compbio-lab/SkillFoundry/skills/systems-biology/reactome-pathway-hierarchy-walk-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Regulatory network inference starter

    ma-compbio-lab/SkillFoundry/skills/systems-biology/regulatory-network-inference-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • String interaction partners starter

    ma-compbio-lab/SkillFoundry/skills/systems-biology/string-interaction-partners-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Bulk rna seq qc and normalization starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/bulk-rna-seq-qc-and-normalization-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Cellxgene census atlas query starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/cellxgene-census-atlas-query-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Isoform transcript level analysis starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/isoform-transcript-level-analysis-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Perturb seq starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/perturb-seq-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Pseudobulk analysis starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/pseudobulk-analysis-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Pydeseq2 differential expression starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/pydeseq2-differential-expression-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Rna velocity starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/rna-velocity-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Scanpy cell type annotation starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/scanpy-cell-type-annotation-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Scanpy combat batch correction starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/scanpy-combat-batch-correction-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Scanpy dpt trajectory starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/scanpy-dpt-trajectory-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Scanpy qc starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/scanpy-qc-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Scanpy ranked genes starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/scanpy-ranked-genes-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Spatial transcriptomics starter

    ma-compbio-lab/SkillFoundry/skills/transcriptomics/spatial-transcriptomics-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Dash scientific dashboard starter

    ma-compbio-lab/SkillFoundry/skills/visualization-and-reporting/dash-scientific-dashboard-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Figure recreation from papers starter

    ma-compbio-lab/SkillFoundry/skills/visualization-and-reporting/figure-recreation-from-papers-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Matplotlib publication plot starter

    ma-compbio-lab/SkillFoundry/skills/visualization-and-reporting/matplotlib-publication-plot-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Mkdocs summary catalog starter

    ma-compbio-lab/SkillFoundry/skills/visualization-and-reporting/mkdocs-summary-catalog-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Plotly interactive report starter

    ma-compbio-lab/SkillFoundry/skills/visualization-and-reporting/plotly-interactive-report-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Quarto notebook report starter

    ma-compbio-lab/SkillFoundry/skills/visualization-and-reporting/quarto-notebook-report-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Skill browser mindmap generation starter

    ma-compbio-lab/SkillFoundry/skills/visualization-and-reporting/skill-browser-mindmap-generation-starter Skill

    36★ repo

    A framework for discovering, compiling, and validating reusable skills for scientific agents.

  • Dangerous config file protection

    ychampion/cskill-agents/agents/claude-code/skills/dangerous-config-file-protection Skill

    36★ repo

    Agent skills for coding CLIs, multi-agent runtimes, context engines, MCP extensions, and terminal tooling. Instead of using claude code's source code, give your agent skills to create your own!

  • Privacy redacted repl bridge system init

    ychampion/cskill-agents/agents/claude-code/skills/privacy-redacted-repl-bridge-system-init Skill

    36★ repo

    Agent skills for coding CLIs, multi-agent runtimes, context engines, MCP extensions, and terminal tooling. Instead of using claude code's source code, give your agent skills to create your own!

  • Shared system init shape parity

    ychampion/cskill-agents/agents/claude-code/skills/shared-system-init-shape-parity Skill

    36★ repo

    Agent skills for coding CLIs, multi-agent runtimes, context engines, MCP extensions, and terminal tooling. Instead of using claude code's source code, give your agent skills to create your own!

  • Dangerous config file protection

    ychampion/cskill-agents/agents/codex/skills/dangerous-config-file-protection Skill

    36★ repo

    Agent skills for coding CLIs, multi-agent runtimes, context engines, MCP extensions, and terminal tooling. Instead of using claude code's source code, give your agent skills to create your own!

  • Privacy redacted repl bridge system init

    ychampion/cskill-agents/agents/codex/skills/privacy-redacted-repl-bridge-system-init Skill

    36★ repo

    Agent skills for coding CLIs, multi-agent runtimes, context engines, MCP extensions, and terminal tooling. Instead of using claude code's source code, give your agent skills to create your own!