[](https://travis-ci.org/lima1/PureCN)
[](https://codecov.io/gh/lima1/PureCN)
[](https://opensource.org/licenses/Artistic-2.0)
# PureCN
A tool developed for tumor-only diagnostic sequencing using hybrid-capture
protocols. It provides copy number adjusted for purity and ploidy and can
classify mutations by somatic status and clonality. It requires a pool of
process-matched normals for coverage normalization and artifact filtering.
PureCN was parameterized using large collections of diverse samples, ranging
from low coverage whole-exome to ultra-deep sequenced plasma gene-panels.
## Installation
To install this package, start R and enter:
```
source("https://bioconductor.org/biocLite.R")
biocLite("PureCN")
```
If your R/Bioconductor version is outdated, this will install an old and
unsupported version.
For outdated R/Bioconductor versions, you can try backporting the latest stable
version (this should work fine for Bioconductor 3.3 and later):
```
biocLite("lima1/PureCN", ref="RELEASE_3_7")
```
If you want the latest and greatest from the developer branch:
```
biocLite("lima1/PureCN")
```
## Tutorials
To get started:
```
vignette("Quick", package="PureCN")
```
For the R package and more detailed information:
```
vignette("PureCN", package="PureCN")
```
These tutorials are also available on the Bioconductor project page ([devel](https://bioconductor.org/packages/devel/bioc/html/PureCN.html), [stable](https://doi.org/doi:10.18129/B9.bioc.PureCN)).
## Paper
Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D and Morrissey M
(2016). “PureCN: Copy number calling and SNV classification using targeted
short read sequencing.” _Source Code for Biology and Medicine_, **11**, pp. 13.
doi: [10.1186/s13029-016-0060-z](http://doi.org/10.1186/s13029-016-0060-z).
---
[](https://postimg.org/image/yer1jeiln/)
Copy number profile obtained by a 500-gene panel.
