title: RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data.
abstract: : 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).
  
  
  
  rshankar@stanford.edu.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Ravi D
authors.initials: RD
authors.lastname: Shankar
authors.affiliation: Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
authors.forename: Sanchita
authors.initials: S
authors.lastname: Bhattacharya
authors.affiliation: Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
authors.forename: Chethan
authors.initials: C
authors.lastname: Jujjavarapu
authors.affiliation: Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Sandra
authors.initials: S
authors.lastname: Andorf
authors.affiliation: Northrop Grumman Information Technology Health Solutions, Rockville, MD 20850, USA.
authors.forename: Jeffery A
authors.initials: JA
authors.lastname: Wiser
authors.affiliation: Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
authors.forename: Atul J
authors.initials: AJ
authors.lastname: Butte
mesh_terms: D000486:Allergy and Immunology; D019295:Computational Biology; D006801:Humans; D012106:Research; D012984:Software