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scatac-analysis

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Analyze single-cell ATAC-seq with Signac/ArchR (R) and SnapATAC2 (Python alternative). Use when processing scATAC fragments, choosing a framework, calling consensus peaks, running TF-IDF/LSI while diagnosing the depth component, scoring chromVAR motif deviations against GC-matched backgrounds, detecting homotypic vs heterotypic doublets, or deciding whether to binarize the count matrix.

When to use

• processing scATAC fragments
• choosing a framework
• calling consensus peaks
• running TF-IDF/LSI
• diagnosing the depth component
• scoring chromVAR motif deviations
• detecting homotypic vs heterotypic doublets
• deciding whether to binarize the count matrix

When not to use

• single-cell single-gene quantitative claims
• using gene activity as a single-cell transcriptome surrogate
• testing differential accessibility on a peak set called from the same clustering

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