Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive…
Single-Cell RNA-seq Quality Control Automated QC workflow for single-cell RNA-seq data following scverse best practices. When to Use This Skill Use when users: Request quality control or QC on single-cell RNA-seq data Want to filter low-quality cells or assess data quality Need QC visualizations or metrics Ask to follow scverse/scanpy best practices Request MAD-based filtering or outlier detection Supported input formats: .h5ad files (AnnData format from scanpy/Python workflows) .h5 files (10X Genomics Cell Ranger output) Default recommendation: Use Approach 1 (complete pipeline) unless the user has specific custom requirements or explicitly requests non-standard filtering logic.
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