non-targeting controls?

hyunhwan-jeong / CB2

CB2 is an R package which provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.

https://cran.r-project.org/web/packages/CB2/index.html

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non-targeting controls? #1

Open AmandaKedaigle opened 5 years ago

AmandaKedaigle commented 5 years ago

Thanks - this looks nice and is so refreshingly easy to install and use! I was wondering if there was a way in CB2 to account for non-targeting control sgRNAs, or if this is not needed? Thanks

hyunhwan-jeong commented 5 years ago

Hello @AmandaKedaigle,

The current version CB² does not have any data correction function using non-targeting control in the latest version of You can look up the p-values of each individual non-targeting sgRNA for the data quality control and I would suggest getting rid of them in your gene-level analysis.

Please share your thought if you want to add some functions in CB² regarding the matters!

Best Regards,

Hyun-Hwan Jeong