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multiome-pipeline

separate

Orchestrates the end-to-end 10x Multiome (paired scRNA + scATAC) pipeline from Cell Ranger ARC output to a jointly-embedded, annotated object, chaining per-modality QC, AMULET fragment-based ATAC doublet detection, per-modality normalization (RNA SCT/PCA; ATAC TF-IDF/LSI), WNN (or MultiVI) integration, joint clustering, RNA-based annotation, and LinkPeaks peak-to-gene linking. Use when enforcing the shared cell-barcode intersection between modalities (cellranger-ARC not -atac), keeping per-modality QC/doublets before the joint embedding, dropping the depth-correlated LSI component, annotating identity from RNA (ATAC is regulatory state), treating peak-to-gene links as correlational hypotheses, or aggregating to pseudobulk for cross-condition DE. Hands mechanism to the single-cell and atac-seq component skills; not a re-teach of any single step.

When to use

• 10x Multiome paired scRNA + scATAC analysis
• Cell Ranger ARC output processing
• Per-modality QC and AMULET doublet detection
• WNN or MultiVI multimodal integration
• Joint clustering and RNA-based annotation
• LinkPeaks peak-to-gene linking
• Pseudobulk aggregation for cross-condition DE

When not to use

• Re-teaching single-step internals
• ATAC-only barcode analysis using cellranger-atac
• Integrating cells missing a modality with WNN

Skill page

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