Informatics and Biocomputing Program, Ontario Institute for Cancer Research.
Department of Medical Biophysics, University of Toronto.
Bioinformatics. 2018 Mar 15;34(6):1034-1036. doi: 10.1093/bioinformatics/btx707.
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.
NanoStringNormCNV is implemented in R and is freely available at http://labs.oicr.on.ca/boutros-lab/software/nanostringnormcnv.
Supplementary data are available at Bioinformatics online.
NanoString 系统是一种成熟的测量 RNA 和 DNA 丰度的技术。尽管它可以估计拷贝数变异，但支持分析这些数据的工具相对较少。为了解决这一差距，我们创建了 NanoStringNormCNV，这是一个用于从 NanoString 数据进行预处理和拷贝数变异调用的 R 包。该软件包实现了用于预处理、质量控制、归一化和拷贝数变异检测的算法。一系列报告和数据可视化方法支持探索性分析。为了证明其效用，我们将其应用于一个新的数据集，该数据集由 41 个前列腺肿瘤和 24 个匹配的正常样本中的 96 个基因组成。
NanoStringNormCNV 是用 R 实现的，可以在 http://labs.oicr.on.ca/boutros-lab/software/nanostringnormcnv 上免费获得。
补充数据可在 Bioinformatics 在线获得。
