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# 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:
```
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("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If your R/Bioconductor version is outdated, this will install an old and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For outdated R/Bioconductor versions, you can try backporting the latest stable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):
```
BiocManager::install("lima1/PureCN", ref="RELEASE_3_8")
```
If you want the latest and greatest from the developer branch:
```
BiocManager::install("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](https://doi.org/10.1186/s13029-016-0060-z).
## Selected citations
Dagogo-Jack et al. (2018). "Tracking the evolution of resistance to ALK tyrosine kinase
inhibitors through longitudinal analysis of circulating tumor DNA". _JCO
Precision Oncology_. doi:
[10.1200/PO.17.00160](https://doi.org/10.1200/PO.17.00160).
Orlando et al. (2018). "Genetic mechanisms of target antigen loss in CAR19 therapy of
acute lymphoblastic leukemia". _Nature Medicine_.
doi: [10.1038/s41591-018-0146-z](https://doi.org/10.1038/s41591-018-0146-z).
Pal et al. (2018). "Efficacy of BGJ398, a fibroblast growth factor receptor 1-3
inhibitor, in patients with previously treated advanced urothelial carcinoma
with FGFR3 alterations". _Cancer Discovery_. doi:
[10.1158/2159-8290.CD-18-0229](https://doi.org/10.1158/2159-8290.CD-18-0229).
Pitt et al. (2018). "Characterization of Nigerian breast cancer reveals
prevalent homologous recombination deficiency and aggressive molecular
features". _Nature Communications_. doi:
[10.1038/s41467-018-06616-0](https://doi.org/10.1038/s41467-018-06616-0).
