Shankar Ravi D, Bhattacharya Sanchita, Jujjavarapu Chethan, Andorf Sandra, Wiser Jeffery A, Butte Atul J
Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
Bioinformatics. 2017 Apr 1;33(7):1101-1103. doi: 10.1093/bioinformatics/btw719.
: Open access to raw clinical and molecular data related to immunological studies has created a tremendous opportunity for data-driven science. We have developed RImmPort that prepares NIAID-funded research study datasets in ImmPort (immport.org) for analysis in R. RImmPort comprises of three main components: (i) a specification of R classes that encapsulate study data, (ii) foundational methods to load data of a specific study and (iii) generic methods to slice and dice data across different dimensions in one or more studies. Furthermore, RImmPort supports open formalisms, such as CDISC standards on the open source bioinformatics platform Bioconductor, to ensure that ImmPort curated study datasets are seamlessly accessible and ready for analysis, thus enabling innovative bioinformatics research in immunology.
RImmPort is available as part of Bioconductor (bioconductor.org/packages/RImmPort).
Supplementary data are available at Bioinformatics online.
开放获取与免疫学研究相关的原始临床和分子数据为数据驱动的科学创造了巨大机遇。我们开发了RImmPort，它可对免疫数据库（immport.org）中由美国国立过敏和传染病研究所资助的研究数据集进行预处理，以便在R语言中进行分析。RImmPort由三个主要部分组成：（i）封装研究数据的R类规范，（ii）加载特定研究数据的基础方法，以及（iii）在一个或多个研究中跨不同维度对数据进行切片和切块的通用方法。此外，RImmPort支持开放形式主义，如开源生物信息学平台Bioconductor上的CDISC标准，以确保免疫数据库中经过整理的研究数据集可无缝访问并随时用于分析，从而推动免疫学领域的创新生物信息学研究。
RImmPort作为Bioconductor的一部分提供（bioconductor.org/packages/RImmPort）。
补充数据可在《生物信息学》在线版获取。
