singlecell-qc

Use when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach. Trigger for scRNA QC metrics, per-sample diagnosis, threshold discussion, mitochondrial/ambient/doublet assessment, MAD vs fixed cutoffs, or refactoring automated merge-first QC. The analyst confirms key decisions at each step—agents must inspect data, propose options, and wait for…