Build Status Coverage License: Artistic-2.0


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.


To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

If your R/Bioconductor version is outdated, this will install an old and unsupported version.

For outdated R/Bioconductor versions, you can try backporting the latest stable version (this should work fine for Bioconductor 3.3 and later):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_11")

If you want the latest and greatest from the developer branch:


To get the lastest stable version from Conda:

conda install -c bioconda bioconductor-purecn=1.18.1


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, stable).


Before posting a bug report:


Selected citations

Dummer et al. (2020). "Combined PD-1, BRAF and MEK inhibition in advanced BRAF-mutant melanoma: safety run-in and biomarker cohorts of COMBI-i". Nature Medicine. doi: 10.1038/s41591-020-1082-2.

Bertucci et al. (2019). "Genomic characterization of metastatic breast cancers". Nature. doi: 10.1038/s41586-019-1056-z.

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.

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.

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.

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.

Try the PureCN package in your browser

Any scripts or data that you put into this service are public.

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.