dmDep: CRISPR knockout dependency data from human cell lines

In Solatar/setR:

Description

Data from DepMap Public 20Q1 downloaded on March 09, 2020

Usage

data(dmDep)

Format

An object of class "cross"; see read.cross.

Details

Description from the DepMap website:

CERES data with principle components strongly related to known batch effects removed, then shifted and scaled per cell line so the median nonessential KO effect is 0 and the median essential KO effect is -1.

Rows: cell lines (Broad IDs)

Columns: genes in the format: HUGO (Entrez)

This Achilles dataset contains the results of genome-scale CRISPR knockout screens for 18,333 genes in 739 cell lines.

Source

DepMap download page

References

DepMap, Broad (2020): DepMap 20Q1 Public. figshare. Dataset doi:10.6084/m9.figshare.11791698.v2. (DepMap website)

Robin M. Meyers, Jordan G. Bryan, James M. McFarland, Barbara A. Weir, ... David E. Root, William C. Hahn, Aviad Tsherniak. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics 2017 October 49:1779–1784. doi:10.1038/ng.3984 (Pubmed)

Dempster, J. M., Rossen, J., Kazachkova, M., Pan, J., Kugener, G., Root, D. E., & Tsherniak, A. (2019). Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines. BioRxiv, 720243 (bioRxiv)

Examples

data(dmDep)
dmDep[1:5,1:5]

Solatar/setR documentation built on Dec. 5, 2020, 10:50 p.m.