README.Rmd

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output: github_document
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knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# Rcongas <a href='caravagnalab.github.io/rcongas'><img src='man/figures/logo.png' align="right" height="120" /></a>

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This is the `(R)CONGAS+` R package, an interface to run the probabilistic methods implemented in the Python
[Congas](https://github.com/Militeee/congas) package using Pyro. These methods implement several statistical models 
to genotype Copy Number Alterations from single-cell RNA and ATAC sequencing, integrating at the same time bulk DNA sequencing.

This package implements S3 objects to preprocess and visualize input single-cell data, create and visualize model fits.
The current package is an extension of the original, single-molecule version; it retains the same name to avoid confusion.

#### Citation
https://doi.org/10.1371/journal.pcbi.1011557
[![](https://img.shields.io/badge/doi-10.1371/journal.pcbi.1011557-red.svg)](https://doi.org/10.1371/journal.pcbi.1011557)

If you use `Rcongas`, please cite these two papers:

* _Genotyping Copy Number Alterations from single-cell RNA sequencing._
Salvatore Milite, Riccardo Bergamin, Giulio Caravagna. [biorXiv preprint](https://www.biorxiv.org/content/10.1101/2021.02.02.429335v1), 2021

* _Multi-molecule genotyping Copy Number Alterations from single-cell sequencing._ Salvatore Milite, Riccardo Bergamin, Lucrezia Patruno, Alex Graudenzi, Giulio Caravagna. 

#### Help and support

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

### Installation

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

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

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#### Copyright and contacts

Salvatore Milite, MSc, Riccardo Bergamin, PhD, and Giulio Caravagna, PhD. _University of Trieste, Trieste, Italy_.

[![](https://img.shields.io/badge/Email-gcaravagn@gmail.com-steelblue.svg)](mailto:gcaravagn@gmail.com)
[![](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/)