Single Cell Rna Qc

Runs the standard scverse QC pipeline on single-cell RNA-seq data with MAD-based filtering and generates before/after visualizations. Works with both h5ad files and 10X h5 outputs. The convenience script handles the full workflow automatically, but you can also use the modular functions if you need different thresholds for cell subsets or want to skip filtering entirely. Default thresholds are intentionally permissive to avoid losing rare populations. Outputs include filtered h5ad files ready for downstream analysis plus PNG plots showing count depth, gene detection, and mitochondrial content. This is the boring foundation work you need to do before anything interesting happens, packaged so you don't have to remember the scanpy incantations.

Install to Claude Code

npx -y skills add anthropics/knowledge-work-plugins --skill single-cell-rna-qc --agent claude-code