Table 4.

Summary of scATAC-seq analysis tools

Tool [Ref]	Feature Matrix	QC	Clustering	Gene activity	DAR	Motif	scRNA-seq integration	Platform
Signac [282]	Peak	YES	YES	YES	YES	NO	Seurat	R
ArchR [283]	Peak/Bin	YES	YES	YES	YES	NO	Seurat	R
chromVAR [275]	TF motifs	YES	YES	NO	NO	YES	NO	R
SnapATAC [284]	Peak/Bin	YES	YES	YES	YES	YES	Seurat	R/Python
cisTopic [277]	Peak	YES	YES	YES	NO	NO	NO	R
SHARE-seq [278]	Peak	YES	YES	YES	NO	YES	Seurat	R
BROCKMAN [285]	Peak	YES	YES	NO	NO	YES	NO	R
AtacWorks [286]	Peak	YES	NO	YES	YES	NO	NO	Python
Destin [287]	Peak	YES	YES	NO	YES	NO	NO	R
EpiScanpy [288]	Peak	YES	YES	NO	NO	NO	NO	Python
Cicero [276]	TSS	YES	YES	YES	YES	NO	NO	R
Scasat [289]	Peak	YES	YES	NO	YES	NO	NO	R/Python
SCRAT [290]	Any	YES	YES	NO	YES	NO	NO	R
SCALE [291]	Peak	YES	YES	NO	YES	YES	NO	Python
ChromSCape [292]	Peak/Bin/TSS	YES	YES	NO	YES	NO	NO	R
Cusanovich2018 [293]	Peak	YES	YES	YES	YES	YES	Seurat	R
scABC [294]	Peak	YES	YES	NO	NO	YES	NO	R
scATAC-pro [295]	Peak	YES	YES	YES	YES	YES	NO	R/Python

QC Quality Control, DAR Differentially accessible region