Dataset Information

NanoStringNormCNV: pre-processing of NanoString CNV data.

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.

SUBMITTER: Sendorek DH

PROVIDER: S-EPMC5860631 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Publications

NanoStringNormCNV: pre-processing of NanoString CNV data.

Sendorek Dorota H DH Lalonde Emilie E Yao Cindy Q CQ Sabelnykova Veronica Y VY Bristow Robert G RG Boutros Paul C PC

Bioinformatics (Oxford, England) 20180301 6

<h4>Summary</h4>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 ...[more]

PMID: 29112706

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Dataset Information

NanoStringNormCNV: pre-processing of NanoString CNV data.

Publications

NanoStringNormCNV: pre-processing of NanoString CNV data.

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