achilles | R Documentation |
The 'achilles' dataset contains the metadata for DepMap’s cancer models/cell lines, specific to Project Achilles’ 22Q2 CRISPR screens. This dataset can be loaded into the R environment with the 'depmap_achilles' function.
achilles
A data frame with 1036 rows and 6 variables:
cancer cancer cell line foreign key (i.e. "ACH-00001")
CCLE name of cancer cell line (i.e. "184A1_BREAST")
Number of replicates used in Achilles CRISPR screen passing QC
Difference in the means of positive and negative controls normalized by the standard deviation of the negative control distribution
Medium used to grow cell line
Percentage of cells remaining GFP negative on days 12-14 of cas9 activity assay as measured by FACs
This data represents the 'Achilles_metadata.csv' file taken from the 22Q2 [Broad Institute](https://depmap.org/portal/download/) release.
- 22Q1: Initial dataset
- 22Q2: "culture_type" column was removed
DepMap, Broad Institute: https://depmap.org/portal/download/
Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A., Kryukov, G., Cowley, G. S., ... & Meyers, R. M. (2017). Defining a cancer dependency map. Cell, 170(3), 564-576.
James M. McFarland, Zandra V. Ho, Guillaume Kugener, Joshua M. Dempster, Phillip G. Montgomery, Jordan G. Bryan, John M. Krill-Burger, Thomas M. Green, Francisca Vazquez, Jesse S. Boehm, Todd R. Golub, William C. Hahn, David E. Root, Aviad Tsherniak. (2018). Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nature Communications 9, 1.
## Not run:
depmap_achilles()
## End(Not run)
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