This repository contains data and executable scripts to reproduce the figures and analysis presented in the paper:
Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL
Peter-Martin Bruch*, Holly A. R. Giles*, Carolin Kolb, Sophie A. Herbst, Tina Becirovic, Tobias Roider, Junyan Lu, Sebastian Scheinost, Lena Wagner, Jennifer Huellein, Ivan Berest, Mark Kriegsmann, Katharina Kriegsmann, Christiane Zgorzelski, Peter Dreger, Judith B. Zaugg, Carsten Müller-Tidow, Thorsten Zenz, Wolfgang Huber*, Sascha Dietrich*
*These authors contributed equally to this work.
The data can be accessed in .RData format in /data and in .txt format in inst/extdata. The scripts can be found in vignettes/src and the assosciated html files (showing the anlaysis in full) in inst/doc. To run the entire analysis, clone the repository and run the script CLLCytokineScreen2021.Rmd. Make sure you have updated R to at least version 4.1.0 and have installed all libraries in CLLCytokineScreen2021.Rmd beforehand.
If you use this analysis in published research, please cite the paper. Please refer to the manuscript for more details on experimental methods and analysis.
The presented analysis was performed by Holly Giles and Peter-Martin Bruch, building on scripts from Sascha Dietrich, Wolfgang Huber, Junyan Lu, Malgorzata Oles, Frederik Ziebell, Sophie Herbst and Ivan Berest. This repository is maintained by Holly Giles. If you have questions, email me at [email protected].
The data can also be explored interactively via the online shiny app.