DepMapScreener

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Authorship

Collin Schlager

Department of Biochemistry
Department of Computer Science
Stanford University
[email protected]

Features

• Virtually screen cancer cell lines using the Broad Institute's DepMap data
• Run virtual knock out screens on multiple genes
• Run virtual expression screens on any percentile of the population
• Run virtual lineage screens to compare cancer types
• Fully stand-alone R-shiny application wrapped in Electron Desktop framework

Download Instructions

1. Click on the releases button in the bar above (the one that has "commits", "branches", and "contributors" on it)
2. Under Assets, download the .dmg file
3. Open the .dmg file
4. At this point, you can click the application to run, or you can click and drag it into the Applications folder to copy it to your computer.
5. Run the app by doubling clicking the icon
   • Depending on your security preferences, your computer may warn you about the app coming from an unidentified developer (that's me)
   • To give the app permissions (you only need to do this once), go into your System Preferences and click on Security and Privacy. There should be dialog box that says the app wants permission to open. Hit Run Anyway.
   • If the app doesn't open, re-run the application by double clicking the icon.

Troubleshooting

1. The app icon isn't loading! It just has a generic icon.
   • This is a known issue and one that will be (hopefully) fixed in the next release
   • You can restore the icon by doing the following:
     1. Right click the DepMapScreener application and click Show Package Contents
     2. Click into the Contents folder
     3. Then click into the following folders Resources/app/assets/icons/png
     4. Double click to open the appIcon.png file in Preview
     5. Select and copy the image contents by hitting Cmd+a and Cmd+c
     6. With the image contents (NOT FILE) copied, go back to the folder with the DepMapScreener application
     7. Single click the main application and hit Cmd+i
     8. Click the little icon on the top right and paste the icon contents in with Cmd+v
     9. You can also try to paste the image contents into the larger icon under the Preview tab

Credit

Inspiration

Edmond M. Chan et al., “WRN Helicase Is a Synthetic Lethal Target in Microsatellite Unstable Cancers,” Nature 568, no. 7753 (April 1, 2019): 551–56, https://doi.org/10.1038/s41586-019-1102-x.

DepMap and Omics Data

DepMap, Broad (2019): DepMap Achilles 19Q1 Public. figshare. Fileset. doi:10.6084/m9.figshare.7655150

Robin M. Meyers, Jordan G. Bryan, James M. McFarland, Barbara A. Weir, ... David E. Root, William C. Hahn, Aviad Tsherniak. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics 2017 October 49:1779–1784. doi:10.1038/ng.3984

Cancer Cell Line Encyclopedia Consortium, and Genomics of Drug Sensitivity in Cancer Consortium. 2015. Pharmacogenomic Agreement between Two Cancer Cell Line Data Sets. Nature 528 (7580):84–87. https://doi.org/10.1038/nature15736.

Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, William R. Sellers, Robert Schlegel, Levi A. Garraway, et. al. 2012. The Cancer Cell Line Encyclopedia Enables Predictive Modelling of Anticancer Drug Sensitivity. Nature 483 (7391):603–7. https://doi.org/10.1038/nature11003.

Framework

The integration of R-Shiny into Electron uses R-Portable and was inspired and adapted from Katie Sasso of the Columbus Collaboratory: https://github.com/ColumbusCollaboratory/electron-quick-start. The template was modified to install and use custom packages locally from an in-app library directory.