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.

Author
Ravi Shankar <rshankar@stanford.edu>
Date of publication
None
Maintainer
Ravi Shankar <rshankar@stanford.edu>
License
GPL-3
Version
1.2.0
URLs

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