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README.Rmd
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README.Rmd
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---
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 -->
[](https://github.com/egeulgen/PANACEA/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/egeulgen/PANACEA?branch=master)
[](https://cran.r-project.org/package=PANACEA)
[](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>*
## 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)