Achilles GeCKO 2.0 release. 

This set includes the results of 43 cell lines screened with the genome-wide GeCKO library . 

Contents:

Gene level data:
gene_effect: Matrix of CERES inferred gene effects normalized so the median of the positive controls is -1 and the median of the negative controls is 0. 
essential_genes, nonessential_genes: positive and negative controls drawn from Hart et al. (https://dx.doi.org/10.152522/msb.20145216)

Guide level data:
replicate_map: map of replicate names to the cell line they were derived from
guide_activity: CERES inferred activity scores for each guide
guide-QCed: ZMADed guide X replicate scores
guide_locus_map: map of sgRNA to genome
locus_gene_map: map of gene to genome
locus_cn: copy number for loci in each cell line


Processing steps:

QC:
1. Drop replicates that do not pass fingerprinting
2. Drop replicates with less than 15 million reads
3. Drop guides with pDNA reads less than 1 millionth of the total pDNA pool
4. Drop any replicates that do not have a pearson correlation > 0.7 with at least one other replicate for the same line
5. Drop replicates with SSMD < -.5. The controls for SSMD are the 217 pan-essential and 841 non-essential genes identified by Hart et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299491/
6. ZMAD by cell line

CERES:
1. Drop cell lines with no available copy number
2. Infer gene effect, guide activity, and copy number effect