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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.