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Table 1 A comparison of MAGeCK with existing shRNA/siRNA screening methods: RIGER, RSA, edgeR and DESeq

From: MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens

 

Methods

MAGeCK

RIGER [14]

RSA [15]

edgeR [7] /DESeq [8]

sgRNA ranking

Ranking method

Negative binomial P-value

Signal-to-noise ratio

Fold change

Negative binomial P-value

Statistical evaluation

Yes

No

No

Yes

Number of samples required in each category

1, prefer more

At least 2

1

1

Bias towards sgRNAs with smaller read countsa

No

No

Yes

No

Gene ranking

Ranking method

Robust rank aggregation P-value

Kolmogorov-Smirnov P-value

Iterative hyper-geometric P-value

Not applied to gene ranking

Permutation

Yes

Yes

No

FDRb

Low

Low

High

Sensitivity in detecting negatively selected genesc

High

Low

High

Robust against the number of sgRNAs/gened

Yes

No

Yes

  1. aEvaluated in Figure S5 in Additional file 1.
  2. bEvaluated in Figure 2a and in Table S1 in Additional file 2.
  3. cEvaluated in Figure 2a and in Table S1 in Additional file 2.
  4. dEvaluated in Figure 5.