achilles: achilles_22Q2

In UCLouvain-CBIO/depmap: Cancer Dependency Map Data Package

achilles_22Q2

Description

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.

Usage

achilles

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.

Change log

- 22Q1: Initial dataset

- 22Q2: "culture_type" column was removed

Source

DepMap, Broad Institute: https://depmap.org/portal/download/

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.

Examples

## Not run: 
depmap_achilles()

## End(Not run)

UCLouvain-CBIO/depmap documentation built on March 24, 2024, 2 p.m.