寡核苷酸微阵列预处理框架。
A framework for oligonucleotide microarray preprocessing.
机构信息
Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
出版信息
Bioinformatics. 2010 Oct 1;26(19):2363-7. doi: 10.1093/bioinformatics/btq431. Epub 2010 Aug 5.
MOTIVATION
The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools.
RESULTS
We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages.
AVAILABILITY
The oligo package is freely available through BioConductor, http://www.bioconductor.org.
动机
可灵活使用的开源软件，用于分析基因表达原始数据，这极大地促进了这些技术中广泛使用的预处理方法的发展。然而，微阵列应用的扩展暴露了现有工具的局限性。
结果
我们开发了 oligo 包，提供了更通用的解决方案，支持广泛的应用。该包基于 BioConductor 的透明性、可重复性和开发效率的原则。它扩展了现有的工具，并利用现有的代码进行可视化、访问数据和广泛使用的预处理例程。oligo 包实现了数据预处理的统一范例，并与其他 BioConductor 工具进行接口，以进行下游分析。我们的基础设施是通用的，可被其他 BioConductor 包使用。
可用性
oligo 包可通过 BioConductor 免费获得，网址为 http://www.bioconductor.org。
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