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.
Format
A data frame with 1036 rows and 6 variables:
- depmap_id
cancer cancer cell line foreign key (i.e. "ACH-00001")
- cell_line
CCLE name of cancer cell line (i.e. "184A1_BREAST")
- achilles_n_replicates
Number of replicates used in Achilles CRISPR screen passing QC
- cell_line_NNMD
Difference in the means of positive and negative controls normalized by the standard deviation of the negative control distribution
- culture_medium
Medium used to grow cell line
- cas9_activity
Percentage of cells remaining GFP negative on days 12-14 of cas9 activity assay as measured by FACs
Details
This data represents the `Achilles_metadata.csv` file taken from the 22Q2 [Broad Institute](https://depmap.org/portal/download/) release.
References
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.