Package: RImmPort 1.35.0

Zicheng Hu

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.

Authors:Ravi Shankar <[email protected]>

RImmPort_1.35.0.tar.gz
RImmPort_1.35.0.zip(r-4.5)RImmPort_1.35.0.zip(r-4.4)RImmPort_1.35.0.zip(r-4.3)
RImmPort_1.35.0.tgz(r-4.4-any)RImmPort_1.35.0.tgz(r-4.3-any)
RImmPort_1.35.0.tar.gz(r-4.5-noble)RImmPort_1.35.0.tar.gz(r-4.4-noble)
RImmPort_1.35.0.tgz(r-4.4-emscripten)RImmPort_1.35.0.tgz(r-4.3-emscripten)
RImmPort.pdf |RImmPort.html✨
RImmPort/json (API)

# Install 'RImmPort' in R:

install.packages('RImmPort', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:RImmPort-1.35.0(bioc 3.21)RImmPort-1.34.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

biomedicalinformatics dataimport datarepresentation

4.33 score 27 scripts 145 downloads 2 mentions 20 exports 36 dependencies

Last updated 2 months agofrom:804fce5619. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 27 2024
R-4.5-win	NOTE	Dec 27 2024
R-4.5-linux	NOTE	Dec 27 2024
R-4.4-win	NOTE	Dec 27 2024
R-4.4-mac	NOTE	Dec 27 2024
R-4.3-win	NOTE	Dec 27 2024
R-4.3-mac	NOTE	Dec 27 2024

Exports:buildNewSqliteDb Events Findings getAssayDataOfStudies getDomainCode getDomainDataOfStudies getListOfAssayTypes getListOfDomains getListOfStudies getStudiesWithSpecificAssayData getStudiesWithSpecificDomainData getStudy Interventions loadSerializedStudyData mergeDomainAndSupplemental serialzeStudyData setImmPortDataSource SpecialPurpose Study TrialDesign

Dependencies:bit bit64 blob cachem chron cli cpp11 data.table DBI dplyr fansi fastmap generics glue gsubfn lifecycle magrittr memoise pillar pkgconfig plogr plyr proto R6 Rcpp reshape2 rlang RSQLite sqldf stringi stringr tibble tidyselect utf8 vctrs withr

RImmPort: Enabling ready-for-analysis immunology research data

Ravi Shankar

Rendered fromRImmPort_Article.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2018-03-30
Started: 2016-02-22

RImmPort: Quick Start Guide

Ravi Shankar

Rendered fromRImmPort_QuickStart.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2018-03-30
Started: 2016-02-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adverse Events Domain	Adverse Events Domain
Adverse Events Domain Variables	AE
Associated Persons Medical History Domain Variables	APMH
Associated Persons Medical History Domain	Associated Persons Medical History Domain
buildNewSqliteDb	buildNewSqliteDb
Cellular Quantification Domain	Cellular Quantification Domain
Concomitant Medications Domain Variables	CM
Concomitant Medications Domain	Concomitant Medications Domain
Demographics Domain	Demographics Domain
Demographics Domain Variables	DM
Protocol Deviations Domain Variables	DV
Events class	Events Events-class
Exposure Domain Variables	EX
Exposure Domain	Exposure Domain
Findings About Domain Variables	FA
Findings About Domain	Findings About Domain
Findings class	Findings Findings-class
Genetics Findings Domain	Genetics Findings Domain
Get specific assay data of one or more studies from the ImmPort database	getAssayDataOfStudies
Get code of a specific domain	getDomainCode
Get specific domain data of one or more studies from the ImmPort database	getDomainDataOfStudies
Get a list of Assay Types	getListOfAssayTypes
Get names of all domains and their codes	getListOfDomains
Get a list of all studies	getListOfStudies
Get a list of studies that have specific assay type data	getStudiesWithSpecificAssayData
Get a list of studies that have specific domain data	getStudiesWithSpecificDomainData
Get all data of a specific study from the ImmPort data source	getStudy
Interventions class	Interventions Interventions-class
Laboratory Test Results Domain	Laboratory Test Results Domain
Laboratory Test Results Domain Variables	LB
Load the Serialized Data of a Study	loadSerializedStudyData
Medical History Domain	Medical History Domain
Merge the Domain dataframe and Supplemental dataframe (long form)	mergeDomainAndSupplemental
Medical History Domain Variables	MH
Nucleic Acid Quantification Domain	Nucleic Acid Quantification Domain
Physical Examination Domain Variables	PE
Genetics Findings Domain Variables	PF
Physical Examination Domain	Physical Examination Domain
Protein Quantification Domain	Protein Quantification Domain
Protocol Deviations Domain	Protocol Deviations Domain
Questionnaires Domain Variables	QS
Questionnaires Domain	Questionnaires Domain
RImmPort: Enabling ready-for-analysis immunology research data	RImmPort-package RImmPort
Serialize the Study Data	serialzeStudyData
Set ImmPort data ource	setImmPortDataSource
Skin Response Domain	Skin Response Domain
Special Purpose class	SpecialPurpose SpecialPurpose-class
Skin Response Domain Variables	SR
Study class	Study Study-class
Substance Use Domain Variables	SU
Subject Visits Domain	Subject Visits Domain
Substance Use Domain	Substance Use Domain
Supplemental Variables	SUPP
Protocol Deviations Domain Supplemental Variables	SUPPDV
Findings About Domain Supplemental Variables	SUPPFA
Laboratory Test Results Domain Supplemental Variables	SUPPLB
Medical History Domain Supplemental Variables	SUPPMH
Physical Examination Domain Supplemental Variables	SUPPPE
Genetics Findings Domain Supplemental Variables	SUPPPF
Vital Signs Domain Supplemental Variables	SUPPVS
Protein Quantification Domain Supplemental Variables	SUPPZA
Cellular Quantification Domain Supplemental Variables	SUPPZB
Nucleic Acid Quantification Domain Supplemental Variables	SUPPZC
Titer Assay Results Domain Supplemental Variables	SUPPZD
Subject Visits Domain Variables	SV
Trial Arms Domain Variables	TA
Trial Inclusion Exclusion Criteria Domain Variables	TI
Titer Assay Results Domain	Titer Assay Results Domain
Trial Arms Domain	Trial Arms Domain
Trial Inclusion Exclusion Criteria Domain	Trial Inclusion Exclusion Criteria Domain
Trial Summary Domain	Trial Summary Domain
Trial Visits Domain	Trial Visits Domain
Trial Design class	TrialDesign TrialDesign-class
Trial Summary Domain Variables	TS
Trial Visits Domain Variables	TV
Vital Signs Domain	Vital Signs Domain
Vital Signs Domain Variables	VS
Protein Quantification Domain Variables	ZA
Cellular Quantification Domain Variables	ZB
Nucleic Acid Quantification Domain Variables	ZC
Titer Assay Results Domain Variables	ZD