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BCR_collagen

Modeling of biochemical relapse-free survival in PCa with expression of collagen-related genes

Figures, Tables, and Supplementary Material

The transcriptomic part of the main manuscript text is available as a MS Word file. Supplementary Material for the transcriptomic part of the manuscript is available as a MS Word file.

PDF files with main paper Figures are available here. PDF files with Supplementary Figures are available here.

Terms of use

Please cite the repository and the peer-reviewed publication, when available. The analysis pipeline is GPL-3 licensed. The raw data files will be made upon request to the senior study authors, Dr. Isabel Heidegger and Dr. Maria Frantzi.

Usage

The following development packages are required to run the pipeline:

## handling of tabular data
devtools::install_github('PiotrTymoszuk/trafo')

## script sourcing
devtools::install_github('PiotrTymoszuk/soucer') 

## exploratory data analysis and statistical hypothesis testing
devtools::install_github('PiotrTymoszuk/ExDA') 
devtools::install_github('PiotrTymoszuk/fastTest')
devtools::install_github('PiotrTymoszuk/microViz')
devtools::install_github('PiotrTymoszuk/clustTools')

## network analyses
devtools::install_github('PiotrTymoszuk/graphExtra')

## management of figures and tables in Rmd documents
devtools::install_github('PiotrTymoszuk/figur')

## handling and analysis of Cox proportional hazard models
devtools::install_github('PiotrTymoszuk/coxExtensions')

Source 'exec.R' to launch the entire pipeline:

source('exec.R')

Contact

The repository maintainer is Piotr Tymoszuk. Data requests should be addressed to Dr. Isabel Heidegger and Dr. Maria Frantzi