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Table 1 Comprehensive features of MAESTRO compared to other single-cell tools

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

✓

✓

✓

✓

✓

✓

✓

✓

✓

✓

✓

✓