Normal bladder urothelium

This repository contains the scripts and data to regenerate the main and extended figures of the manuscript titled: "Sex and smoking influence selection of somatic mutations in human bladder".

Ferriol Calvet1,4,6, Raquel Blanco Martinez-Illescas1,4,6, Ferran Muiños1,4, Maria Tretiakova2, Elena S. Latorre-Esteves2, Jeanne Fredrickson2, Maria Andrianova1, Stefano Pellegrini1,4, Axel Rosendahl Huber1, Joan Enric Ramis-Zaldivar1,4, Shuyi (Charlotte) An2, Elana Thieme2, Brendan F. Kohrn2, Miguel Grau1, Abel Gonzalez-Perez1,4,5,7, Nuria Lopez-Bigas1,3,4,5,7, Rosa Ana Risques2,7

1. These authors contributed equally and the order was decided randomly: R. Blanco Martinez-Illescas, F. Calvet

2. These authors jointly supervised this work: A. Gonzalez-Perez, N. Lopez-Bigas, R. Risques

Correspondence should be addressed to Nuria Lopez-Bigas nuria.lopez@irbbarcelona.org and Rosa Ana Risques rrisques@uw.edu

Affiliations

1. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
2. Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA.
3. Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
4. Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
5. Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.

Reproducibility

Code

All the code required for regenerating the figures is available here in this repo, and should be run in Python (version >=3.10). We provide a requirements list that includes at least the required packages for running the codes.

Data

All the data required for regenerating the figures is available in the following either in this repo directly or in the Zenodo repo : DOI:10.5281/zenodo.15836679

Once downloaded and uncompressed, the absolute path to this data should be use to update the variable all_data_path in the consensus_variables.py file.

Data access

Note that the data for generating some of the figures has been shared in an aggregated manner for privacy concerns.

The access to specific datasets for 3 panels is still restricted and we are working to provide a processed version of the data that can be used for the full reproducibility of these missing panels. All the code is already available.