The R scripts require the following R packages to be installed:
- CRISPRcleanR
- preprocessCore
- stringr
- sva
- tsne
- vcd
- reshape
- qvalue
- dendextend
- colorspace
- RColorBrewer
- matrixStats
- ggplot2
- ggrepel
- ggpubr
- beeswarm
- qusage
All python scripts are contained in comparative_analysis.ipynb. This file requires jupyter notebook to open, and the following packages:
- numpy
- scipy
- pandas
- matplotlib
- seaborn
- sklearn
- statsmodels
- adjustText
The scripts also require input data to be downloaded from Figshare: https://figshare.com/articles/Agreement_between_two_large_pan-cancer_CRISPR-Cas9_gene_dependency_datasets/7970993/1. To run the R scripts see the Initialise_script.R. This also requires the working directory to be set to the location of the Pipeline folder in this directory. The InputFolder directory needs to be set to the path where the downloaded data from Figshare is stored. To run the python scripts, launch jupyter notebook and open comparative_analysis.ipynb. You will need to edit the second cell under the subheading Read In to point to the path where the figshare data was downloaded.