R/Shiny web app to calculate injection mix volumes for CRISPR-Cas9 experiments.
Link to web app: http://imlspenticton.uzh.ch:3838/CrispantCal
CRISPR-Cas9 is a revolutionary experimental technique for genome editing. For a scientific overview, see this review (also available as a PDF). For a less technical introduction, you can find a large number of articles and videos on the internet, for example this article by Wired or many videos on YouTube.
This web app calculates optimal injection mix volumes for CRISPR-Cas9 experiments in the lab. It is designed to be easily accessible from a laptop or phone while preparing experiments.
CrispantCal was developed using the Shiny web application framework for the R programming language.
The CrispantCal web app can be accessed with a desktop or mobile browser at: http://imlspenticton.uzh.ch:3838/CrispantCal
An alternative link is available at: https://lmweber.shinyapps.io/CrispantCal. This version is hosted online using the shinyapps.io service by RStudio. However, this link may be unavailable sometimes due to limited monthly hours of usage.
The CrispantCal app can also be installed locally and run from an R session in RStudio with the R command runGitHub("lmweber/CrispantCal"). This requires the shiny package to be installed and loaded first, which can be done with the commands install.packages("shiny") and library(shiny).
If you are not familiar with R, we recommend RStudio as a user-friendly editor. You will also need to download R from CRAN. Introductory tutorials are available from the RStudio website.
Once you have installed R and RStudio, open RStudio and paste the commands above into the Console window, which is on the left or in the bottom left corner of the screen in the default layout. The CrispantCal app should then launch in a new window or in the Viewer pane on the right.
Note that on Mac OSX Yosemite, the wget utility may cause errors with the runGitHub command. This can be fixed by uninstalling wget.
Instructions on how to use the CrispantCal calculator and details about the calculations are shown in the Information section on the main page of the app.
CrispantCal was introduced in the following paper. See the paper for details about the scientific context.
Source code and local installation files are available on GitHub at: lmweber/CrispantCal
Developed by Lukas M. Weber, Jonas Zaugg, Anastasia Felker, and Christian Mosimann (Mark D. Robinson and Christian Mosimann labs), Institute of Molecular Life Sciences, University of Zurich, Switzerland.
For citations, please use the paper above (Burger et al., 2016).