Introduction

Data analysis of Impact of neoadjuvant chemotherapy on local breast microbiota and macrophages in ER-positive breast cancer: shifts in density, composition, and links to treatment response funded by Academisch Alliantie Fonds Maastricht UMC+ and Radboudumc.

The current data analysis was performed with an R version of 4.3.3, the renv will try to sync the R package versions with your current R version, please make sure renv is available on your local machine. Unfortunately, using a conda environment doesn't work with all R packages, therefore I will leave the R version restrictions to the users end.

You can install all required R packages via renv::restore() or you might be prompted to do so at the beginning, see the docs for more information.

Running the data-analysis workflow

Note

The data is available upon requests from the paper.

Make sure you have the folders data with the neccessary input files from the paper. You can also manually edit the R/00_main.R file to change the filepaths.

Rscript R/00_main.R

Code that was used to for phylogenetic tree reconstruction

mpirun -n 20 phyml-mpi -i pseudomonas_BRAAF.phylip -d nt --model K80 --alpha 0.2890 -f 0.25,0.25,0.25,0.25 -c 4 -b 100

Support

Please open an issue if you need any support.