SGDI：基因组数据整合系统。
SGDI: system for genomic data integration.
作者信息
Carey V J, Gentry J, Sarkar R, Gentleman D, Ramaswamy S
机构信息
Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA.
出版信息
Pac Symp Biocomput. 2008:141-52. doi: 10.1142/9789812776136_0016.
This paper describes a framework for collecting, annotating, and archiving high-throughput assays from multiple experiments conducted on one or more series of samples. Specific applications include support for large-scale surveys of related transcriptional profiling studies, for investigations of the genetics of gene expression and for joint analysis of copy number variation and mRNA abundance. Our approach consists of data capture and modeling processes rooted in R/Bioconductor, sample annotation and sequence constituent ontology management based in R, secure data archiving in PostgreSQL, and browser-based workspace creation and management rooted in Zope. This effort has generated a completely transparent, extensible, and customizable interface to large archives of high-throughput assays. Sources and prototype interfaces are accessible at www.sgdi.org/software.
本文描述了一个用于收集、注释和存档在一个或多个系列样本上进行的多个实验的高通量检测的框架。具体应用包括支持相关转录谱研究的大规模调查、基因表达遗传学研究以及拷贝数变异和mRNA丰度的联合分析。我们的方法包括基于R/Bioconductor的数据捕获和建模过程、基于R的样本注释和序列组成本体管理、PostgreSQL中的安全数据存档以及基于Zope的基于浏览器的工作区创建和管理。这项工作为高通量检测的大型存档生成了一个完全透明、可扩展且可定制的界面。可在www.sgdi.org/software上访问数据源和原型界面。
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