PhenoDriverR

R package for identifying personalized driver genes and exploring their oncogenic mechanism

Installation

PhenoDriverR depends on org.Hs.eg.db, DESeq2, AnnotationDbi, clusterProfiler R packages from Bioconductor and please make sure they are installed before installing PhenoDriverR. An R version >= 4.1 is suggested.

To speed up matrix product, it is highly recommended to install openblas library first. For ubuntu, run the following command:

sudo apt install libopenblas-dev

Install the required packages

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install(c("org.Hs.eg.db", "DESeq2", "AnnotationDbi", "clusterProfiler")

Install PhenoDriver

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("NWPU-903PR/PhenoDriverR")

Data required

PhenoDriverR needs personalized gene expression and mutation data to identify driver genes. In addition, a weighted and directed Signal Tranduction Network (STN) also required for PhenoDriver workflow. Breast cancer data, as an example, can be found in another github repository

Usage of PhenoDriverR

See the R Script for an example of PhenoDriver full process execution.