README.Rmd

---
output: github_document
---

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

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

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`CNAqc` is a package that contains different methods to inspect the quality, visualise and process allele-specific Copy Number Alteration (CNA) calls generated from bulk sequencing of tumour samples, jointly with tumour somatic mutations and other covariates. 

Methods are available to integrate somatic mutation data,  clonal and subclonal CNA segments, and tumour purity estimates. Quality control procedures can be easily used to select among alternative tumour segmentations and purity/ ploidy estimates; an automatic pipeline to optimize CNA calling is available by interfacing CNAqc with Sequenza. The package provides also methods to estimate the Cancer Cell Fractions (CCFs) values of the input variants, and estimate their uncertainty. The package contains also statistical tests to identify patterns of over-fragmentation of chromosome arms, smooth and subset segments, and annotate putative driver mutations.

#### Citation

[![](https://img.shields.io/badge/doi-10.1101/2021.02.13.429885-red.svg)](https://doi.org/10.1101/2021.02.13.429885)

If you use `CNAqc`, please cite:

* _Integrated quality control of allele-specific copy numbers, mutations and tumour purity from cancer whole genome sequencing assays_
  Jacob Househam, Riccardo Bergamin, Salvatore Milite, Nicola Calonaci, Alice Antonello, Marc J Williams, William CH Cross, Giulio Caravagna. [biorXiv 2022](https://www.biorxiv.org/content/10.1101/2021.02.13.429885v3).


#### Help and support

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

You can install the released version of `CNAqc` with:

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

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#### Copyright and contacts

Giulio Caravagna. 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/)