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single-cell-atac

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Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

When to use

• 10X scATAC data processing
• 10X Multiome paired RNA+ATAC data
• per-cell QC
• choosing between ArchR/Signac/SnapATAC2 ecosystems
• building per-cluster consensus peaksets
• integrating with paired scRNA-seq
• doublet detection
• pseudobulk differential accessibility per cluster

When not to use

• scATAC-pro legacy pipelines

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