Table 1 |.

Main functions of MAGeCKFlute

Functions	Description of functions
mageck count	Map the raw FASTQ data to reference library file and count the reads for each sgRNA
mageck test	MAGeCK RRA (identifying CRISPR screen hits by calculating the RRA enrichment score to indicate the essentiality of a gene)
mageck mle	MAGeCK MLE (identifying CRISPR screen hits by calculating a ‘beta score’ for each targeted gene to measure the degree of selection after the target is perturbed)
VISPR	Visualisation of the result of MAGeCK.
mageck-vispr	Quality control at the FASTQ and raw count level. Includes all the functions of MAGeCK and VISPR
BatchRemove	Remove batch effect of CRISPR screen data at the raw read count level
mageck test/mle --cnv-norm parameter	Correct the bias caused by copy number when identifying hits with MAGeCK RRA and MAGeCK MLE.
mageck_nest.py	Improve hit identification and remove outlier sgRNAs
FluteRRA	Downstream analysis of the MAGeCK RRA results
FluteMLE	Quality control at the beta score level; normalization with essential genes; identify drug treatment related hits; functional analysis