NOTE. This script has been developed for the following publication:
The script compares and finds the sgRNA sequences with desired features combining CRISPR-ERA (Liu et al, 2015), Yeast CRISPRi (Smith et al, 2016), and CHOPCHOP (Labun et al, 2019). Script available also in the "sgRNA-Donor-Design_Script.pdf" file (with descriptions and dataframes embedded in the code).
Getting started:
- Install RMarkdown in RStudio. No need of pre-installing the other packages needed for the script as they will be installed automatically (if they are not already).
- Check the data organisation in the example file provided in the Input folder (Data_Example_Analysis.xlsx). Replicate in the same way an input file with the desired genes.
- Download the script and place it in the same folder of the file to be analysed. The excel file name should end with "Analysis" and should be a .xlsx file. Changes in the script can be made to import other file formats.
- Open the script and follow the directions. Make changes upon need (replace grouping variables, fluorescence analysis, dimentions of images, etc.).
Luca Torello Pianale, lucat@chalmers.se, Industrial Biotechnology Division, Chalmers University of technology
Created: December, 2023.
The scripts were tested with: R Version 4.3.0 (2023-04-21 ucrt) - RStudio (2021.09.2 Build 382)
Acknowledgment of support: This material is based upon work supported by the Novo Nordisk Foundation grant DISTINGUISHED INVESTIGATOR 2019 - Research within biotechnology-based synthesis & production (#0055044).