scATAC-seq in R
Carry one Signac object through fragment-aware QC, LSI, peak testing, motif enrichment, and optional chromVAR.
- Input
- Peak counts, cell metadata, indexed fragments, and gene annotation.
- Analysis unit
- Cell for QC and markers; sample for condition peak tests.
- Outputs
- Signac object, QC, LSI, peak tests, motif enrichment, and optional chromVAR scores.
- Key limit
- Genome build and coordinates must match across peaks, fragments, annotation, and sequence resources.