RImmPort: RImmPort: Enabling Ready-for-analysis Immunology Research Data

The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.

AuthorRavi Shankar <rshankar@stanford.edu>
Date of publicationNone
MaintainerRavi Shankar <rshankar@stanford.edu>
LicenseGPL-3
Version1.2.0
http://bioconductor.org/packages/RImmPort/

View on Bioconductor

Man pages

Adverse-Events-Domain: Adverse Events Domain

AE: Adverse Events Domain Variables

APMH: Associated Persons Medical History Domain Variables

Associated-Persons-Medical-History-Domain: Associated Persons Medical History Domain

buildNewSqliteDb: buildNewSqliteDb

Cellular-Quantification-Domain: Cellular Quantification Domain

CM: Concomitant Medications Domain Variables

Concomitant-Medications-Domain: Concomitant Medications Domain

Demographics-Domain: Demographics Domain

DM: Demographics Domain Variables

DV: Protocol Deviations Domain Variables

Events-class: Events class

EX: Exposure Domain Variables

Exposure-Domain: Exposure Domain

FA: Findings About Domain Variables

Findings-About-Domain: Findings About Domain

Findings-class: Findings class

Genetics-Findings-Domain: Genetics Findings Domain

getAssayDataOfStudies: Get specific assay data of one or more studies from the...

getDomainCode: Get code of a specific domain

getDomainDataOfStudies: Get specific domain data of one or more studies from the...

getListOfAssayTypes: Get a list of Assay Types

getListOfDomains: Get names of all domains and their codes

getListOfStudies: Get a list of all studies

getStudiesWithSpecificAssayData: Get a list of studies that have specific assay type data

getStudiesWithSpecificDomainData: Get a list of studies that have specific domain data

getStudy: Get all data of a specific study from the ImmPort data source

Interventions-class: Interventions class

Laboratory-Test-Results-Domain: Laboratory Test Results Domain

LB: Laboratory Test Results Domain Variables

loadSerializedStudyData: Load the Serialized Data of a Study

Medical-History-Domain: Medical History Domain

mergeDomainAndSupplemental: Merge the Domain dataframe and Supplemental dataframe (long...

MH: Medical History Domain Variables

Nucleic-Acid-Quantification-Domain: Nucleic Acid Quantification Domain

PE: Physical Examination Domain Variables

PF: Genetics Findings Domain Variables

Physical-Examination-Domain: Physical Examination Domain

Protein-Quantification-Domain: Protein Quantification Domain

Protocol-Deviations-Domain: Protocol Deviations Domain

QS: Questionnaires Domain Variables

Questionnaires-Domain: Questionnaires Domain

RImmPort: RImmPort: Enabling ready-for-analysis immunology research...

serialzeStudyData: Serialize the Study Data

setImmPortDataSource: Set ImmPort data ource

Skin-Response-Domain: Skin Response Domain

SpecialPurpose-class: Special Purpose class

SR: Skin Response Domain Variables

Study-class: Study class

SU: Substance Use Domain Variables

Subject-Visits-Domain: Subject Visits Domain

Substance-Use-Domain: Substance Use Domain

SUPP: Supplemental Variables

SUPPDV: Protocol Deviations Domain Supplemental Variables

SUPPFA: Findings About Domain Supplemental Variables

SUPPLB: Laboratory Test Results Domain Supplemental Variables

SUPPMH: Medical History Domain Supplemental Variables

SUPPPE: Physical Examination Domain Supplemental Variables

SUPPPF: Genetics Findings Domain Supplemental Variables

SUPPVS: Vital Signs Domain Supplemental Variables

SUPPZA: Protein Quantification Domain Supplemental Variables

SUPPZB: Cellular Quantification Domain Supplemental Variables

SUPPZC: Nucleic Acid Quantification Domain Supplemental Variables

SUPPZD: Titer Assay Results Domain Supplemental Variables

SV: Subject Visits Domain Variables

TA: Trial Arms Domain Variables

TI: Trial Inclusion Exclusion Criteria Domain Variables

Titer-Assay-Results-Domain: Titer Assay Results Domain

Trial-Arms-Domain: Trial Arms Domain

TrialDesign-class: Trial Design class

Trial-Inclusion-Exclusion-Criteria-Domain: Trial Inclusion Exclusion Criteria Domain

Trial-Summary-Domain: Trial Summary Domain

TS: Trial Summary Domain Variables

Vital-Signs-Domain: Vital Signs Domain

VS: Vital Signs Domain Variables

ZA: Protein Quantification Domain Variables

ZB: Cellular Quantification Domain Variables

ZC: Nucleic Acid Quantification Domain Variables

ZD: Titer Assay Results Domain Variables

Files in this package

RImmPort/DESCRIPTION
RImmPort/NAMESPACE
RImmPort/R
RImmPort/R/AdverseEvents.R RImmPort/R/ArrayResults.R RImmPort/R/AssociatedPersonsMedicalHistory.R RImmPort/R/CellularQuantification.R RImmPort/R/ConcomitantMedications.R RImmPort/R/Demographics.R RImmPort/R/ElisaResults.R RImmPort/R/ElispotResults.R RImmPort/R/Exposure.R RImmPort/R/FcsResults.R RImmPort/R/FindingsAbout.R RImmPort/R/GeneticsFindings.R RImmPort/R/HaiResults.R RImmPort/R/HlaTypingResults.R RImmPort/R/ImmPortSqlite.R RImmPort/R/LaboratoryTestResults.R RImmPort/R/MbaaResults.R RImmPort/R/MedicalHistory.R RImmPort/R/NeutAbTiterResults.R RImmPort/R/NucleicAcidQuantification.R RImmPort/R/PcrResults.R RImmPort/R/PhysicalExamination.R RImmPort/R/ProteinQuantification.R RImmPort/R/ProtocolDeviations.R RImmPort/R/Questionnaires.R RImmPort/R/RImmPort.R RImmPort/R/SkinResponse.R RImmPort/R/Study.R RImmPort/R/SubjectBasicAnalyses.R RImmPort/R/SubjectVisits.R RImmPort/R/SubstanceUse.R RImmPort/R/TiterAssayResults.R RImmPort/R/TrialArms.R RImmPort/R/TrialInclusionExclusionCriteria.R RImmPort/R/TrialSummary.R RImmPort/R/VitalSigns.R
RImmPort/build
RImmPort/build/vignette.rds
RImmPort/inst
RImmPort/inst/doc
RImmPort/inst/doc/RImmPort_Article.R
RImmPort/inst/doc/RImmPort_Article.Rmd
RImmPort/inst/doc/RImmPort_Article.pdf
RImmPort/inst/doc/RImmPort_QuickStart.R
RImmPort/inst/doc/RImmPort_QuickStart.Rmd
RImmPort/inst/doc/RImmPort_QuickStart.pdf
RImmPort/inst/extdata
RImmPort/inst/extdata/ImmPortStudies
RImmPort/inst/extdata/ImmPortStudies/Db
RImmPort/inst/extdata/ImmPortStudies/Db/ImmPort.sqlite
RImmPort/inst/extdata/ImmPortStudies/Rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/dm.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppdm.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppta.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppts.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppzb.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppzc.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/ta.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/ts.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/zb.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/zc.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/dm.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppdm.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppta.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppts.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppza.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppzb.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppzd.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/ta.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/ts.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/za.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/zb.rds
RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/zd.rds
RImmPort/inst/extdata/ImmPortStudies/Tab
RImmPort/inst/extdata/ImmPortStudies/Tab/SDY139-DR16_Tab.zip
RImmPort/inst/extdata/ImmPortStudies/Tab/SDY208-DR16_Tab.zip
RImmPort/man
RImmPort/man/AE.Rd RImmPort/man/APMH.Rd RImmPort/man/Adverse-Events-Domain.Rd RImmPort/man/Associated-Persons-Medical-History-Domain.Rd RImmPort/man/CM.Rd RImmPort/man/Cellular-Quantification-Domain.Rd RImmPort/man/Concomitant-Medications-Domain.Rd RImmPort/man/DM.Rd RImmPort/man/DV.Rd RImmPort/man/Demographics-Domain.Rd RImmPort/man/EX.Rd RImmPort/man/Events-class.Rd RImmPort/man/Exposure-Domain.Rd RImmPort/man/FA.Rd RImmPort/man/Findings-About-Domain.Rd RImmPort/man/Findings-class.Rd RImmPort/man/Genetics-Findings-Domain.Rd RImmPort/man/Interventions-class.Rd RImmPort/man/LB.Rd RImmPort/man/Laboratory-Test-Results-Domain.Rd RImmPort/man/MH.Rd RImmPort/man/Medical-History-Domain.Rd RImmPort/man/Nucleic-Acid-Quantification-Domain.Rd RImmPort/man/PE.Rd RImmPort/man/PF.Rd RImmPort/man/Physical-Examination-Domain.Rd RImmPort/man/Protein-Quantification-Domain.Rd RImmPort/man/Protocol-Deviations-Domain.Rd RImmPort/man/QS.Rd RImmPort/man/Questionnaires-Domain.Rd RImmPort/man/RImmPort.Rd RImmPort/man/SR.Rd RImmPort/man/SU.Rd RImmPort/man/SUPP.Rd RImmPort/man/SUPPDV.Rd RImmPort/man/SUPPFA.Rd RImmPort/man/SUPPLB.Rd RImmPort/man/SUPPMH.Rd RImmPort/man/SUPPPE.Rd RImmPort/man/SUPPPF.Rd RImmPort/man/SUPPVS.Rd RImmPort/man/SUPPZA.Rd RImmPort/man/SUPPZB.Rd RImmPort/man/SUPPZC.Rd RImmPort/man/SUPPZD.Rd RImmPort/man/SV.Rd RImmPort/man/Skin-Response-Domain.Rd RImmPort/man/SpecialPurpose-class.Rd RImmPort/man/Study-class.Rd RImmPort/man/Subject-Visits-Domain.Rd RImmPort/man/Substance-Use-Domain.Rd RImmPort/man/TA.Rd RImmPort/man/TI.Rd RImmPort/man/TS.Rd RImmPort/man/Titer-Assay-Results-Domain.Rd RImmPort/man/Trial-Arms-Domain.Rd RImmPort/man/Trial-Inclusion-Exclusion-Criteria-Domain.Rd RImmPort/man/Trial-Summary-Domain.Rd RImmPort/man/TrialDesign-class.Rd RImmPort/man/VS.Rd RImmPort/man/Vital-Signs-Domain.Rd RImmPort/man/ZA.Rd RImmPort/man/ZB.Rd RImmPort/man/ZC.Rd RImmPort/man/ZD.Rd RImmPort/man/buildNewSqliteDb.Rd RImmPort/man/getAssayDataOfStudies.Rd RImmPort/man/getDomainCode.Rd RImmPort/man/getDomainDataOfStudies.Rd RImmPort/man/getListOfAssayTypes.Rd RImmPort/man/getListOfDomains.Rd RImmPort/man/getListOfStudies.Rd RImmPort/man/getStudiesWithSpecificAssayData.Rd RImmPort/man/getStudiesWithSpecificDomainData.Rd RImmPort/man/getStudy.Rd RImmPort/man/loadSerializedStudyData.Rd RImmPort/man/mergeDomainAndSupplemental.Rd RImmPort/man/serialzeStudyData.Rd RImmPort/man/setImmPortDataSource.Rd
RImmPort/vignettes
RImmPort/vignettes/RImmPort_Article.Rmd
RImmPort/vignettes/RImmPort_Components.png
RImmPort/vignettes/RImmPort_Process.png
RImmPort/vignettes/RImmPort_QuickStart.Rmd

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