From: Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Methods | Multiple technologies (e.g., scRNA-seq, scATAC-seq) | Multiple platforms (e.g., 10X Genomics, sci-ATAC-seq) | Alignment | Bulk level QC | Single-cell QC | Expression index and peak calling | Normalization | Clustering | Differential analysis | Cell-type annotation | Regulator annotation | Integrated analysis between multiple technologies |
---|---|---|---|---|---|---|---|---|---|---|---|---|
SC3 [19] | ✓ | ✓ | ✓ | |||||||||
SNN-cliq [20] | ✓ | ✓ | ✓ | |||||||||
MAST [22] | ✓ | ✓ | ||||||||||
scde [21] | ✓ | ✓ | ||||||||||
Monocle [27] | ✓ | ✓ | ✓ | ✓ | ✓ | |||||||
Pagoda [34] | ✓ | ✓ | ✓ | ✓ | ✓ | |||||||
Scanpy [29] | ✓ | ✓ | ✓ | ✓ | ✓ | |||||||
Seurat [28] | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |||||
scABC [23] | ✓ | ✓ | ✓ | |||||||||
CisTopic [24] | ✓ | ✓ | ✓ | ✓ | ||||||||
chromVAR [25] | ✓ | ✓ | ✓ | ✓ | ||||||||
Cicero [26] | ✓ | ✓ | ✓ | ✓ | ||||||||
Cellranger [16] | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
Dr.seq2 [18] | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||
snapATAC [17] | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |||
MAESTRO | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |