Table 1 The execution time of mcRigor (in min) for detecting dubious metacells and optimizing metacell method-hyperparameter configuration

From: mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis

   

Detecting dubious metacells

 

Optimizing metacell partitioning

Dataset

# cell

γ

SEACells

MetaCell

MetaCell2

SuperCell

γ

SEACells

MetaCell

MetaCell2

SuperCell

   

Original

mcRigor

Original

mcRigor

Original

mcRigor

Original

mcRigor

 

Original

mcRigor

Original

mcRigor

Original

mcRigor

Original

mcRigor

COVID-19 PBMC

3028

50

5.646

0.185

3.840

0.232

0.367

0.216

0.162

0.186

2–100

920.064

8.788

225.412

7.382

17.281

7.734

17.283

8.962

scMulitome

6800

100

9.519

1.319

—

—

—

—

3.705

1.355

2–200

>1000

91.183

—

—

—

—

743.041

104.013

Semi-synthetic

13400

50

3.001

1.620

2.066

1.543

2.830

1.782

1.712

1.695

2–100

>1000

136.022

220.464

125.906

327.598

116.879

167.522

148.076

Dropseq + smRNA FISH

8498

50

58.608

0.721

4.057

0.673

2.394

0.659

1.956

0.801

2–100

>1000

75.586

479.197

68.833

200.246

73.795

193.688

75.281

scRNA-seq + bulk ESC

350

30

0.568

0.192

0.821

0.173

—

—

0.038

0.153

2–50

26.562

4.070

39.654

3.247

—

—

1.935

3.646

Zman-seq

2431

50

4.749

0.185

1.341

0.167

0.578

0.185

0.219

0.177

2–100

774.616

8.284

154.848

7.926

30.493

7.383

22.242

7.925

  1. Column names: “original”: the time for implementing the original metacell methods; “mcRigor”: the time for applying mcRigor to the generated metacell partition(s). “—” indicates the method is not applicable to the data (MetaCell and MetaCell2 are inapplicable to the scATAC-seq modality in “scMultiome” dataset; MetaCell2 is inapplicable to the “scRNA-seq + bulk ESC” dataset due to the small number of cells).
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