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%"
)
```

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

<!-- badges: start -->
[![R-CMD-check](https://github.com/caravagnalab/INCOMMON/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/caravagnalab/INCOMMON/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->

INCOMMON is a tool for the INference of COpy number and Mutation Multiplicity in ONcology.
INCOMMON infers the copy number and multiplicity of somatic mutations from tumor-only read count data, 
and can be applied to classify mutations from large-size datasets in an efficient and fast way. 

INCOMMON is also available as a user-friendly [ShinyApp](https://ncalonaci.shinyapps.io/incommon/).

Check out our preprint on [medRxiv](doi.org/10.1101/2024.05.13.24307238)!

    
#### Help and support

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

## Installation

You can install the INCOMMON from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("caravagnalab/INCOMMON")
```

#### Copyright and contacts

Cancer Data Science (CDS) Laboratory.

[![](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/)