CCLE.gisticCNA: Genome-wide copy number data for 13 human cancer cell lines.

In francescojm/CRISPRcleanR: Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting

Genome-wide copy number data for 13 human cancer cell lines.

Description

Genome-wide Gistic [1] scores quantifying copy number status across a subset of the cell lines in CL.subset that are used to assess CRISPRcleaneR results in [2].

Usage

data(CCLE.gisticCNA)

Format

A data frame with one observations per gene across 13 variables (one per cell line). Row names indicate HGNC gene symbols and column names indicate cell line COSMIC identifiers [3].

Source

This data frame has been derived from the tsv file downloadable at
http://www.cbioportal.org/study?id=cellline_ccle_broad#summary.
This has been obtained by processing Affymetrix SNP array data in the Cancer Cell Line Encyclopaedia [4] repository
(https://depmap.org/portal/download/)

References

[1] Mermel CH, Schumacher SE, Hill B, et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011;12(4):R41. doi: 10.1186/gb-2011-12-4-r41.

[2] Iorio, F., Behan, F. M., Goncalves, E., Beaver, C., Ansari, R., Pooley, R., et al. (n.d.). Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.
http://doi.org/10.1101/228189

[2] Forbes SA, Beare D, Boutselakis H, et al. COSMIC: somatic cancer genetics at high-resolution Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D777-D783,

[3] Barretina J, Caponigro G, Stransky N, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003. Erratum in: Nature. 2012 Dec 13;492(7428):290.

Examples

data(CCLE.gisticCNA)
head(CCLE.gisticCNA)

francescojm/CRISPRcleanR documentation built on April 30, 2023, 5:41 a.m.