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/PANACEA/blob/master/inst/extdata/PANACEA_logo.png?raw=true" align="left" height="150/"/> PANACEA: Personalized Network-based Anti-Cancer Therapy Evaluation

<!-- badges: start -->

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

Identification of the most appropriate pharmacotherapy for each patient based on genomic alterations is a major challenge in personalized oncology. `PANACEA` is a collection of personalized anti-cancer drug prioritization approaches utilizing network methods. The methods utilize personalized "driverness" scores from [`driveR`](https://egeulgen.github.io/driveR/) to rank drugs, mapping these onto a protein-protein interaction network. The "distance-based" method scores each drug based on these scores and distances between drugs and genes to rank given drugs. The "RWR" method propagates these scores via a random-walk with restart framework to rank the drugs.

The method is described in detail in *Ulgen E, Ozisik O, Sezerman OU. PANACEA: network-based methods for pharmacotherapy prioritization in personalized oncology. Bioinformatics. 2023 Jan 1;39(1):btad022. <https://doi.org/10.1093/bioinformatics/btad022>*

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

## Installation

You can install the latest release version of PANACEA from CRAN via:

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

You can install the development version of PANACEA from GitHub with:

``` r
# install.packages("devtools") @ if you don't have devtools installed
devtools::install_github("egeulgen/PANACEA", build_vignettes = TRUE)
```

## Usage

The wrapper function `score_drugs()` can be used to score and rank drugs for an individual tumor sample via the "distance-based" or "RWR" method. The required inputs are:

-   `driveR_res`: data frame of [driveR](https://egeulgen.github.io/driveR/) results. Details on how to obtain `driveR` output are provided in [this vignette](https://egeulgen.github.io/driveR/articles/how_to_use.html)
-   `drug_interactions_df`: data frame of drug-gene interactions (defaults to interactions from DGIdb expert-curated sources)
-   `W_mat`: (symmetric) adjacency matrix for the protein interaction network (defaults to STRING v11.5 interactions with combined score \> .4)
-   `method`: scoring method (one of "distance-based" or "RWR")

## Example Usage

For detailed information on how to use `PANACEA`, please see the vignette "How to use PANACEA" via `vignette("how_to_use")` or visit [this link](https://egeulgen.github.io/PANACEA/articles/how_to_use.html)