Software used for phosphoproteomics analysis in the manuscript (soon to be published).
Maintainer: Marek Gierlinski
Collaborators: Elisenda Raga Gil, Kate Storey
The software in this repository is build as a targets pipeline in R. We recommend using Positron or RStudio for running the pipeline.
Open an R console in Positron or RStudio and create the environment using renv:
install.packages("renv")
renv::restore()This will install all the required packages. If anything is missing, install additional packages locally using renv::install(). You can check if all packages are installed by running source("_targets.R"). If no errors are produced, you are good to go.
Once the environment is set up, run the targets pipeline:
targets::tar_make()This will perform all calculations, generate data objects, figures, and tables (as targets objects), and output TSV files in the ./tab directory. An HTML report will be generated in the ./doc directory.