RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data | Zendy

Ravi Shankar | Zendy; Sanchita Bhattacharya | Zendy; Chethan Jujjavarapu | Zendy; Sandra Andorf | Zendy; Jeffery A Wiser | Zendy; Atul J. Butte | Zendy

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RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data

Author(s) -

Ravi Shankar,

Sanchita Bhattacharya,

Chethan Jujjavarapu,

Sandra Andorf,

Jeffery A Wiser,

Atul J. Butte

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw719

Subject(s) - bioconductor , computer science , r package , dice , rotation formalisms in three dimensions , raw data , data mining , open source , software , data science , software engineering , bioinformatics , programming language , biology , biochemistry , geometry , mathematics , gene

: 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.

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