Overview - MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK can be used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK identifies both positively and negatively selected genes simultaneously and reports robust results across different experimental conditions. MAGeCK is developed and maintained by Wei Li and Han Xu from Prof. Xiaole Shirley Liu’s lab at the Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health. MAGeCK has been used to identify functional lncRNAs from screens with close to 100% validation rate.
Our goal with our platform is to bring a one-stop no-code interface to each of these workflows. We would love to hear about how you use this workflow and what you use it for so we can improve the experience along the road.
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How to run MAGeCK on Latch
On Latch we have split up the MAGeCK workflow into its subcommands to be run. These are:
MAGeCK - Count
MAGeCK - Test
MAGeCK - MLE
MAGeCK - Pathway
MAGeCK - Plot
You can get an overview on how these subcommands work and feed into one another through this graph:
mageck-subcommand-input-output-graph.pdf
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We would love to hear from you on how you use MAGeCK to better streamline the use of each of the different subcommands. We would like to better understand which subcommands you use, how you use them together and what would improve your MAGeCK experience.
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