This folder contains the code used in The Mutational Footprints of Cancer Therapies. If you use this code in a publication, please cite:
Citation
Oriol Pich, Ferran Muiños, Martijn Paul Lolkema, Neeltje Steeghs, Abel Gonzalez-Perez, Nuria Lopez-Bigas, The mutational footprints of cancer therapies, Nature Genetics, 2019, doi
As part of this work we didn’t generate any original data. We re-used publicly available data described in specific sections of the methods. The metastatic tumor cohort data (DR-024 version 2) is available from the Hartwig Medical Foundation for academic research upon request. Without the Hartwig Metastatic tumor cohort the results won't be reproducible.
These analysis have been perform using software in Python, R, Julia, and GNU bash.
We have created a set of Jupyter notebooks that you can run if you are interested in re-running partially or totally our analysis. In each notebook you will find further details for running them.
To be able to run those notebooks you need to have the following software installed:
- Software requirements: Instructions to install requeriments
We divided the analyses in different parts. Please look at the different jupyter notebooks which will point to the commands needed for reproducing the analysis.
- preprocessing: Creates and preprocesses some files.
- formatting and annotating: Formats mutation files and annotates them.
- signature extraction: Extracts mutational signatures.
- drugs preprocessing: Processing the drugs administered to the patients before the biopsy
- regression analysis: Perform the logistic regression on treatment-signatures.
- mutational toxicity: Calculate the mutational toxicity per sample.
- timing analysis: Get the early/late, clonal/subclonal activity per mutational signature.
- leishmania treated analysis: Analyze leishmania samples treated with 5-FU.
- signature mixing: Explore the putative components of mutational signatures.
- extended_figures: Perform extra analyses presented in Extended Data Figures.
Each folder contains a notebook with a brief description and the requirements (notebooks that would need to be executed before).
If you would like to reproduce a specific figure, the following notebook will direct you to the analysis that generates it.
- figures: Locates each figure to the respective analysis notebook.
We also provide the code to reproduce the simulations performed in the supplementary materials here.