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

Functions

Adverse Events Domain Man page
AE Man page
APMH Man page
Associated Persons Medical History Domain Man page
buildNewSqliteDb Man page
Cellular Quantification Domain Man page
CM Man page
Concomitant Medications Domain Man page
Demographics Domain Man page
DM Man page
DV Man page
Events Man page
Events-class Man page
EX Man page
Exposure Domain Man page
FA Man page
Findings Man page
Findings About Domain Man page
Findings-class Man page
Genetics Findings Domain Man page
getAssayDataOfStudies Man page
getDomainCode Man page
getDomainDataOfStudies Man page
getListOfAssayTypes Man page
getListOfDomains Man page
getListOfStudies Man page
getStudiesWithSpecificAssayData Man page
getStudiesWithSpecificDomainData Man page
getStudy Man page
Interventions Man page
Interventions-class Man page
Laboratory Test Results Domain Man page
LB Man page
loadSerializedStudyData Man page
Medical History Domain Man page
mergeDomainAndSupplemental Man page
MH Man page
Nucleic Acid Quantification Domain Man page
PE Man page
PF Man page
Physical Examination Domain Man page
Protein Quantification Domain Man page
Protocol Deviations Domain Man page
QS Man page
Questionnaires Domain Man page
RImmPort Man page
RImmPort-package Man page
serialzeStudyData Man page
setImmPortDataSource Man page
Skin Response Domain Man page
SpecialPurpose Man page
SpecialPurpose-class Man page
SR Man page
Study Man page
Study-class Man page
SU Man page
Subject Visits Domain Man page
Substance Use Domain Man page
SUPP Man page
SUPPDV Man page
SUPPFA Man page
SUPPLB Man page
SUPPMH Man page
SUPPPE Man page
SUPPPF Man page
SUPPVS Man page
SUPPZA Man page
SUPPZB Man page
SUPPZC Man page
SUPPZD Man page
SV Man page
TA Man page
TI Man page
Titer Assay Results Domain Man page
Trial Arms Domain Man page
TrialDesign Man page
TrialDesign-class Man page
Trial Inclusion Exclusion Criteria Domain Man page
Trial Summary Domain Man page
TS Man page
Vital Signs Domain Man page
VS Man page
ZA Man page
ZB Man page
ZC Man page
ZD Man page

Files

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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