High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue
Here you will find all the scripts that were used in both the (pre)processing of scCUTseq data and to make all the figures that are associated to the manuscript 'High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue'. You can access all the code and it's output here: https://bicrolab.github.io/scCUTseq
If you wish to run any of the code yourself, simply clone the repository and (interactively) run the R Markdown files. Due to the size of the processed data, the data can be downloaded from figshare. Simply download the data and extract it in your cloned repository.
If there are any issues, please send an email to luuk.harbers@scilifelab.se
The processing and analysis scripts have been run on Ubuntu 20.4, all steps should also be possible to run on mac (and even windows using WSL) but this has not been tested. but this has not been tested. Detailed software versions used can be found in the last chapter here.