README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# <img src="https://github.com/egeulgen/driveR/blob/master/inst/extdata/driveR_logo.png?raw=true" align="left" height=150/> driveR: An R Package for Prioritizing Cancer Driver Genes Using Genomics Data

<!-- badges: start -->
[![CRAN version](http://www.r-pkg.org/badges/version-ago/driveR)](https://cran.r-project.org/package=driveR)
[![R-CMD-check](https://github.com/egeulgen/driveR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/egeulgen/driveR/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/egeulgen/driveR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/egeulgen/driveR?branch=master)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
<!-- badges: end -->

Cancer genomes contain large numbers of somatic alterations but few genes drive tumor development. Identifying cancer driver genes is critical for precision oncology. Most of current approaches either identify driver genes based on mutational recurrence or using estimated scores predicting the functional consequences of mutations. 

`driveR` is a tool for personalized or batch analysis of genomics data for driver gene prioritization by combining genomics information and prior biological knowledge. As features, driveR uses coding impact metaprediction scores, non-coding impact scores, somatic copy number alteration scores, hotspot gene/double-hit gene condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG pathways. It uses these features to estimate cancer-type-specific probabilities for each gene of being a cancer driver using the related task of a multi-task learning classification model.

The method is described in detail in _Ülgen E, Sezerman OU. driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. BMC Bioinformatics. 2021 May 24;22(1):263.[https://doi.org/10.1186/s12859-021-04203-7](https://doi.org/10.1186/s12859-021-04203-7)_ 

## Installation

You can install the latest released version of `driveR` from CRAN via:

```r
install.packages("driveR")
```


You can install the development version of `driveR` from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("egeulgen/driveR", build_vignettes = TRUE)
```

## Usage

![driveR workflow](https://github.com/egeulgen/driveR/blob/master/inst/extdata/driver_workflow.png?raw=true "driveR workflow")

`driveR` has two main objectives:

1. Prediction of **impact of coding variants** (achieved via `predict_coding_impact()`)
2. **Prioritization of cancer driver genes** (achieved via `create_features_df()` and `prioritize_driver_genes()`)

Note that `driveR` require operations outside of R and depends on the outputs from the external tools `ANNOVAR` and `phenolyzer`.

For detailed information on how to use `driveR`, please see the vignette "How to use driveR" via `vignette("how_to_use")`