CRISPulator

A pooled genetic screen simulator

Pooled screens are very useful, but it is difficult to select all of the necessary parameters a priori. This work aims to explore the importance of various screen parameters and the relevance of design choices on the downstream analysis and interpretation.

Setup

To run the simulation, you will need a recent version of Julia installed and in your PATH. Then navigate into the root directory of the project and run julia. Run the following command:

$ julia -e 'Pkg.update(); Pkg.add("Crispulator")'

this copies Crispulator over to the Julia package directory and installs all of its dependencies. Note the $ just represents the prompt, you don't need to type it. Make sure to run the tests and verify that everything is passing

$ julia -e 'Pkg.test("Crispulator")'

Quickstart

For most simple cases, no writing of Julia code is necessary. See the Tutorial for using Crispulator in this manner.

Advanced

See the Custom Simulations for a step-by-step guide to writing a custom simulation on top of Crispulator. Additionally, the Simulation Internals page has in-depth documentation needed for more advanced usage