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ID: hellowind777/helloagents/~commit
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- scanpyStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
- remove-technical-debtGuided journey from a large aged codebase everyone fears to touch to one that is safe to change, legible, bounded, and resilient - paid down in place without a rewrite. Orchestrates eight skills phase by phase - working-with-legacy-code, refactoring-patterns, clean-code, software-design-philosophy, clean-architecture, pragmatic-programmer, release-it, domain-driven-design - asking the user questions at every decision point and recording results in the project docs/ folder (TESTING.md, TECH-DEBT.md, REMOVE-TECHNICAL-DEBT-PLAN.md) so the journey resumes across sessions. Use when the user wants to tame a legacy codebase, pay down technical debt safely, avoid a big-bang rewrite, or says ''we are afraid to touch this code''. For a fresh vibe-coded prototype, improve-code-quality; for greenfield structure, design-code-architecture; for a product-and-UX pass, improve-app; to optimize a working codebase for speed, architecture-optimization. For one framework in isolation, invoke that skill directly.
- graphDeterministic orchestration graph runtime - declarative DAG pipelines with journal-based crash recovery
- gtarsUse Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and the CLI.
- tailwind-v4-shadcn|
- open-setsProblem-solving strategies for open sets in topology