This is the code repository for Revisiting Evidence for Epigenetic Control of Alternative Splicing. Since the code in this repository conducts genome-wide analyses of 405 reference epigenomes, there is no small demo dataset available, but after running the first script, a file with the respective paths on the EpiATLAS FTP server is written, which can be subsequently downloaded.
Most analyses are done in R using the .Rmd files in this repo. To keep track of R package versions, we use renv. To restore this project's versions, which are documented in the renv.lock, use renv::restore().
Some analyses use other languages. For those, we have a mamba/conda environment with the documented versions in env.yml that you can restore using mamba env create -f env.yml.
Please run the scripts in the order indicated by the number with which the files start. The first notebook is 01-gather-data.Rmd and the last one is 10-experimental-events.Rmd.
You can adjust parameters for your local machine in the .Rprofile file.