README.Rmd

---
output: github_document
---


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

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# revolver <a href='caravagn.github.io/revolver'><img src='man/figures/logo.png' align="right" height="139" /></a>

The `revolver` package implements the statistical model described in [PMID: 30171232](https://www.ncbi.nlm.nih.gov/pubmed/30171232) to determine trajectories of repeated evolution from multi-region sequencing data of human cancers.The package implements functions to process data from large cohorts, and determine different types of phylogenetic trees from the input data of each input patients. The package provides also several functions to plot the data and determine clusters of patients that share repeated evolutionary trajectories; this provides a method to stratify cancer patients for the way their tumour evolve, reconciling tumour heterogeneity both between and within patients.
  
  
#### Citation

If you use `revolver`, please cite:

* G. Caravagna, Y. Giarratano, D. Ramazzoti, I. Tomlinson, T.A. Graham, G. Sanguinetti, A. Sottoriva. *Detecting repeated cancer evolution from multi-region tumor sequencing data.* Nature Methods 15, 707–714 (2018). 

[![](https://img.shields.io/badge/doi-10.1038/s41592--018--0108--x-red.svg)](https://doi.org/10.1038/s41592-018-0108-x)

#### Help and support

[![](https://img.shields.io/badge/GitHub%20Pages-https://caravagnalab.github.io/revolver/-yellow.svg)](https://caravagnalab.github.io/revolver)

-----

### Installation

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

``` r
# install.packages("devtools")
devtools::install_github("caravagnalab.github.io/revolver")
```

-----

#### Copyright and contacts

Cancer Data Science (CDS) Laboratory. University of Trieste, Italy.

[![](https://img.shields.io/badge/CDS%20Lab%20Github-caravagnalab-seagreen.svg)](https://github.com/caravagnalab)
[![](https://img.shields.io/badge/CDS%20Lab%20webpage-https://www.caravagnalab.org/-red.svg)](https://www.caravagnalab.org/)