IGVF API R client

The R client is autogenerated based on this IGVF OpenAPI specification, which exposes search, collection, and other read endpoints from the IGVF Data Portal.

Note while the API endpoints are relatively stable, the underlying data model is still evolving, and changing fields/types can cause breaking changes. The latest version of the client reflects the latest version of the schema used by the API.

• API version: 57.0.4
• Package version: 57.0.4
• Generator version: 7.7.0
• Build package: org.openapitools.codegen.languages.RClientCodegen

Installation

Prerequisites

Install the dependencies

install.packages("jsonlite")
install.packages("httr")
install.packages("base64enc")

Install the package

To install directly from Github, use remotes:

install.packages("remotes")
library(remotes)
install_github("IGVF-DACC/igvf-r-client@v57.0.4")

Or clone the repo and build:

git clone https://github.com/IGVF-DACC/igvf-r-client
cd igvf-r-client
R CMD build .
R CMD check igvfclient_57.0.4.tar.gz --no-manual
R CMD INSTALL --preclean igvfclient_57.0.4.tar.gz

To install the package from a local file:

install.packages("igvfclient_57.0.4.tar.gz", repos = NULL, type = "source")

Examples

# Import client
library("igvfclient")

# Instantiate new API instance
api <- IgvfApi$new()

# Search for Software that matches query "abc".
r <- api$Search(query="abc", type=list("Software"))

# Print total number of results and list of results in `@graph`.
print(r$total)
print(r$`@graph`)

# Pull first item, unwrap to underlying Software item with `actual_instance`.
software_item <- r$`@graph`[[1]]$actual_instance

# Print Software item and specific fields.
print(software_item)
print(software_item$`@id`)
print(software_item$description)

# Get the Lab item based on the lab @id in the Software item.
lab <- api$GetById(software_item$lab)

# Print lab and specific field.
print(lab)
print(lab$title)

See other examples in examples.ipynb and test_endpoints.R.

Refer to the documentation for a full specification of endpoint inputs and outputs and model fields.

Documentation for API Endpoints

General Endpoints

All URIs are relative to https://api.data.igvf.org

Class	Method	HTTP request	Description
IgvfApi	Search	GET /search	Search for items on the IGVF Data Portal.
IgvfApi	Schemas	GET /profiles	Retrieve JSON schemas for all item types
IgvfApi	SchemaForItemType	GET /profiles/{item_type}	Retrieve JSON schema for item type
IgvfApi	Report	GET /multireport.tsv	Generate a TSV file report based on search query. All results are returned.
IgvfApi	GetById	GET /{resource_id}	Get item information
IgvfApi	Download	GET /{file_id}/@@download	Download file.
IgvfApi	BatchDownload	GET /batch-download	List files to download based on search query. All results are returned.

Collection Endpoints

All URIs are relative to https://api.data.igvf.org

Class	Method	HTTP request	Description
IgvfApi	AccessKeys	GET /access-keys/@@listing	List items in the AccessKey collection.
IgvfApi	AlignmentFiles	GET /alignment-files/@@listing	List items in the AlignmentFile collection.
IgvfApi	AnalysisSets	GET /analysis-sets/@@listing	List items in the AnalysisSet collection.
IgvfApi	AnalysisStepVersions	GET /analysis-step-versions/@@listing	List items in the AnalysisStepVersion collection.
IgvfApi	AnalysisSteps	GET /analysis-steps/@@listing	List items in the AnalysisStep collection.
IgvfApi	AssayTerms	GET /assay-terms/@@listing	List items in the AssayTerm collection.
IgvfApi	AuxiliarySets	GET /auxiliary-sets/@@listing	List items in the AuxiliarySet collection.
IgvfApi	Awards	GET /awards/@@listing	List items in the Award collection.
IgvfApi	Biomarkers	GET /biomarkers/@@listing	List items in the Biomarker collection.
IgvfApi	ConfigurationFiles	GET /configuration-files/@@listing	List items in the ConfigurationFile collection.
IgvfApi	ConstructLibrarySets	GET /construct-library-sets/@@listing	List items in the ConstructLibrarySet collection.
IgvfApi	CrisprModifications	GET /crispr-modifications/@@listing	List items in the CrisprModification collection.
IgvfApi	CuratedSets	GET /curated-sets/@@listing	List items in the CuratedSet collection.
IgvfApi	DegronModifications	GET /degron-modifications/@@listing	List items in the DegronModification collection.
IgvfApi	Documents	GET /documents/@@listing	List items in the Document collection.
IgvfApi	Genes	GET /genes/@@listing	List items in the Gene collection.
IgvfApi	GenomeBrowserAnnotationFiles	GET /genome-browser-annotation-files/@@listing	List items in the GenomeBrowserAnnotationFile collection.
IgvfApi	HumanDonors	GET /human-donors/@@listing	List items in the HumanDonor collection.
IgvfApi	ImageFiles	GET /image-files/@@listing	List items in the ImageFile collection.
IgvfApi	Images	GET /images/@@listing	List items in the Image collection.
IgvfApi	InVitroSystems	GET /in-vitro-systems/@@listing	List items in the InVitroSystem collection.
IgvfApi	InstitutionalCertificates	GET /institutional-certificates/@@listing	List items in the InstitutionalCertificate collection.
IgvfApi	Labs	GET /labs/@@listing	List items in the Lab collection.
IgvfApi	MatrixFiles	GET /matrix-files/@@listing	List items in the MatrixFile collection.
IgvfApi	MeasurementSets	GET /measurement-sets/@@listing	List items in the MeasurementSet collection.
IgvfApi	ModelFiles	GET /model-files/@@listing	List items in the ModelFile collection.
IgvfApi	ModelSets	GET /model-sets/@@listing	List items in the ModelSet collection.
IgvfApi	MultiplexedSamples	GET /multiplexed-samples/@@listing	List items in the MultiplexedSample collection.
IgvfApi	OpenReadingFrames	GET /open-reading-frames/@@listing	List items in the OpenReadingFrame collection.
IgvfApi	Pages	GET /pages/@@listing	List items in the Page collection.
IgvfApi	PhenotypeTerms	GET /phenotype-terms/@@listing	List items in the PhenotypeTerm collection.
IgvfApi	PhenotypicFeatures	GET /phenotypic-features/@@listing	List items in the PhenotypicFeature collection.
IgvfApi	PlatformTerms	GET /platform-terms/@@listing	List items in the PlatformTerm collection.
IgvfApi	PredictionSets	GET /prediction-sets/@@listing	List items in the PredictionSet collection.
IgvfApi	PrimaryCells	GET /primary-cells/@@listing	List items in the PrimaryCell collection.
IgvfApi	Publications	GET /publications/@@listing	List items in the Publication collection.
IgvfApi	ReferenceFiles	GET /reference-files/@@listing	List items in the ReferenceFile collection.
IgvfApi	RodentDonors	GET /rodent-donors/@@listing	List items in the RodentDonor collection.
IgvfApi	SampleTerms	GET /sample-terms/@@listing	List items in the SampleTerm collection.
IgvfApi	SequenceFiles	GET /sequence-files/@@listing	List items in the SequenceFile collection.
IgvfApi	SignalFiles	GET /signal-files/@@listing	List items in the SignalFile collection.
IgvfApi	Software	GET /software/@@listing	List items in the Software collection.
IgvfApi	SoftwareVersions	GET /software-versions/@@listing	List items in the SoftwareVersion collection.
IgvfApi	Sources	GET /sources/@@listing	List items in the Source collection.
IgvfApi	TabularFiles	GET /tabular-files/@@listing	List items in the TabularFile collection.
IgvfApi	TechnicalSamples	GET /technical-samples/@@listing	List items in the TechnicalSample collection.
IgvfApi	Tissues	GET /tissues/@@listing	List items in the Tissue collection.
IgvfApi	Treatments	GET /treatments/@@listing	List items in the Treatment collection.
IgvfApi	Users	GET /users/@@listing	List items in the User collection.
IgvfApi	WholeOrganisms	GET /whole-organisms/@@listing	List items in the WholeOrganism collection.
IgvfApi	Workflows	GET /workflows/@@listing	List items in the Workflow collection.

Documentation for Models

• AccessKey
• AccessKeyResults
• AlignmentFile
• AlignmentFileResults
• AnalysisSet
• AnalysisSetResults
• AnalysisStep
• AnalysisStepResults
• AnalysisStepVersion
• AnalysisStepVersionResults
• AssayTerm
• AssayTermResults
• Attachment
• Attachment1
• AuxiliarySet
• AuxiliarySetResults
• Award
• AwardResults
• Biomarker
• BiomarkerResults
• ConfigurationFile
• ConfigurationFileResults
• ConstructLibrarySet
• ConstructLibrarySetResults
• CrisprModification
• CrisprModificationResults
• CuratedSet
• CuratedSetResults
• DegronModification
• DegronModificationResults
• Document
• DocumentResults
• Gene
• GeneLocation
• GeneLocation1
• GeneResults
• GenomeBrowserAnnotationFile
• GenomeBrowserAnnotationFileResults
• HumanDonor
• HumanDonorResults
• Image
• ImageFile
• ImageFileResults
• ImageResults
• InVitroSystem
• InVitroSystemResults
• InstitutionalCertificate
• InstitutionalCertificateResults
• Item
• ItemType
• Lab
• LabResults
• Limit
• Locus
• Locus1
• MatrixFile
• MatrixFileResults
• MeasurementSet
• MeasurementSetResults
• ModelFile
• ModelFileResults
• ModelSet
• ModelSetResults
• MultiplexedSample
• MultiplexedSampleResults
• NoResultsResponse
• NoResultsResponseColumnsValue
• NoResultsResponseFacetGroupsInner
• NoResultsResponseFacetsInner
• NoResultsResponseFacetsInnerTermsInner
• NoResultsResponseFiltersInner
• NoResultsResponseSortValue
• OpenReadingFrame
• OpenReadingFrameResults
• Page
• PageLayout
• PageLayoutComponents
• PageResults
• PhenotypeTerm
• PhenotypeTermResults
• PhenotypicFeature
• PhenotypicFeatureResults
• PlatformTerm
• PlatformTermResults
• PredictionSet
• PredictionSetResults
• PrimaryCell
• PrimaryCellResults
• Publication
• PublicationResults
• ReferenceFile
• ReferenceFileResults
• RelatedDonor
• RodentDonor
• RodentDonorResults
• SampleTerm
• SampleTermResults
• SearchFacet
• SearchResultItem
• SearchResults
• SequenceFile
• SequenceFileResults
• SignalFile
• SignalFileResults
• Software
• SoftwareResults
• SoftwareVersion
• SoftwareVersionResults
• Source
• SourceResults
• TabularFile
• TabularFileResults
• TechnicalSample
• TechnicalSampleResults
• Tile
• Tissue
• TissueResults
• Treatment
• TreatmentResults
• User
• UserResults
• WholeOrganism
• WholeOrganismResults
• Workflow
• WorkflowResults

Documentation for Authorization

Authentication schemes defined for the API:

basicAuth

• Type: HTTP basic authentication