RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data.
| Autor: | Shankar RD; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Bhattacharya S; Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA 94158, USA., Jujjavarapu C; Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA 94158, USA., Andorf S; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA., Wiser JA; Northrop Grumman Information Technology Health Solutions, Rockville, MD 20850, USA., Butte AJ; Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA 94158, USA. |
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| Jazyk: | angličtina |
| Zdroj: | Bioinformatics (Oxford, England) [Bioinformatics] 2017 Apr 01; Vol. 33 (7), pp. 1101-1103. |
| DOI: | 10.1093/bioinformatics/btw719 |
| Abstrakt: | Summary: : 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. Availability and Implementation: RImmPort is available as part of Bioconductor (bioconductor.org/packages/RImmPort). Contact: rshankar@stanford.edu. Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com) |
| Databáze: | MEDLINE |
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