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Bioinformatics. 2018 Mar 15;34(6):1034-1036. doi: 10.1093/bioinformatics/btx707.

NanoStringNormCNV: pre-processing of NanoString CNV data.

Author information

1
Informatics and Biocomputing Program, Ontario Institute for Cancer Research.
2
Department of Medical Biophysics, University of Toronto.
3
Princess Margaret Cancer Centre, University Health Network.
4
Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.

Abstract

Summary:

The NanoString System is a well-established technology for measuring RNA and DNA abundance. Although it can estimate copy number variation, relatively few tools support analysis of these data. To address this gap, we created NanoStringNormCNV, an R package for pre-processing and copy number variant calling from NanoString data. This package implements algorithms for pre-processing, quality-control, normalization and copy number variation detection. A series of reporting and data visualization methods support exploratory analyses. To demonstrate its utility, we apply it to a new dataset of 96 genes profiled on 41 prostate tumour and 24 matched normal samples.

Availability and implementation:

NanoStringNormCNV is implemented in R and is freely available at http://labs.oicr.on.ca/boutros-lab/software/nanostringnormcnv.

Contact:

paul.boutros@oicr.on.ca.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
29112706
PMCID:
PMC5860631
[Available on 2019-03-15]
DOI:
10.1093/bioinformatics/btx707

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