collagen_pca

Expression, biological and clinical relevance of the collagen pathway genes in prostate carcinoma

Summary and results

To access manuscript files, please use the following links:

• a Word file with main manuscript tables, figures and parts of methods

• a Word file with manuscript supplementary material

• PDF files with main manuscript figures

• PDF files with supplementary manuscript figures

• an Excel file with manuscript supplementary tables

• extra ROC statistics for proteomic SVM models and visualizations of confusion matrices for PIRADS3 patients

Terms of use

Publicly available data sets were analyzed. To reference and use analysis results, please cite our GitHub repository and our publication if available. In any questions, please contact Isabel Heidegger or Piotr Tymoszuk.

Usage

To make sure to install required development packages prior to runing the pipeline:

devtools::install_github('PiotrTymoszuk/ExDA')
devtools::install_github('PiotrTymoszuk/kmOptimizer')
devtools::install_github('PiotrTymoszuk/coxExtensions')
devtools::install_github('PiotrTymoszuk/trafo')
devtools::install_github('PiotrTymoszuk/clustTools')
devtools::install_github('PiotrTymoszuk/soucer')
devtools::install_github('PiotrTymoszuk/figur')
devtools::install_github('PiotrTymoszuk/caretExtra')
devtools::install_github('PiotrTymoszuk/xena')
devtools::install_github('PiotrTymoszuk/gseaTools')

To launch the entire pipeline, source the exec.R file:

source('exec.R')

Contact

The maintainer of the repository is Piotr Tymoszuk.