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scrnaseq-pipeline

separate

Orchestrates the end-to-end single-cell RNA-seq pipeline from 10x Cell Ranger output to annotated cell types, chaining ambient-RNA removal, doublet detection, MAD-adaptive QC, normalization, integration, clustering, marker annotation, and (separately) pseudobulk DE + differential abundance. Use when honoring the made-once counting commitments (reference build/Ensembl vintage, --include-introns, cell-calling, feature namespace), ordering correct-then-detect-then-normalize (ambient before doublet before normalize), running per-sample QC before merge, integrating-then-clustering (never testing on integrated values), aggregating to pseudobulk for condition DE instead of cells-as-replicates, or pairing DE with differential abundance. Hands mechanism to the single-cell component skills; not a re-teach of any single step.

When to use

• single-cell RNA-seq pipeline orchestration
• ambient-RNA removal
• doublet detection
• MAD-adaptive QC
• normalization and batch integration
• clustering and marker annotation
• pseudobulk DE and differential abundance
• hashing demultiplexing

When not to use

• re-teaching any single step mechanism
• differential expression on integrated values
• cells-as-replicates for condition DE

Skill page

Source