Function reference

Helper functions

Functions that assist you with the overall experience of rbioapi

rba_options(): Set rbioapi Global Options

rba_connection_test(): Test if the Supported Services Are Responding

rba_pages(): Get Multiple Pages of a Paginated Resource

Enrichr (rba_enrichr_*)

Functions that connect you to Enrichr (Gene list enrichment analysis tool) API resources.

rba_enrichr(): A One-step Wrapper for Gene-list Enrichment Using Enrichr

rba_enrichr_add_list(): Upload Your Gene-List to Enrichr

rba_enrichr_enrich(): Get Enrichr Enrichment Results

rba_enrichr_gene_map(): Find Enrichr Terms That Contain a Given Gene

rba_enrichr_libs(): Retrieve a List of available libraries from Enrichr

rba_enrichr_view_list(): View an Uploaded Gene List

JASPAR (rba_jaspar_*)

Functions that connect you to JASPAR (Database of transcription factor binding profiles) API resources.

rba_jaspar_collections(): List collections available in JASPAR

rba_jaspar_collections_matrices(): List matrices available in a JASPAR collection

rba_jaspar_matrix(): Get a Position Frequency Matrices (PFM) with annotations

rba_jaspar_matrix_search(): Search matrix profiles available in JASPAR

rba_jaspar_matrix_versions(): List matrix profile versions associated with a base ID

rba_jaspar_releases(): Get information about JASPAR database releases

rba_jaspar_sites(): Get binding sites of a matrix profile

rba_jaspar_species(): List available species in JASPAR

rba_jaspar_species_matrices(): List matrices available in JASPAR of a species

rba_jaspar_taxons(): List available taxonomic groups in JASPAR

rba_jaspar_taxons_matrices(): List matrices available in JASPAR of a taxonomic group

rba_jaspar_tffm(): Get a TF flexible models (TFFMs) information

rba_jaspar_tffm_search(): Search TF flexible models (TFFMs) available in JASPAR

miEAA (rba_mieaa_*)

Functions that connect you to miEAA (miRNA Enrichment Analysis and Annotation Tool) API resources.

rba_mieaa_cats(): Get Supported Enrichment Categories for a Species and miRNA Type

rba_mieaa_convert_type(): Convert Between Mature and precursor miRNA Accession

rba_mieaa_convert_version(): Convert miRNA accession Between Different miRBase Versions

rba_mieaa_enrich(): A One-step Wrapper for miRNA Enrichment Using miEAA

rba_mieaa_enrich_results(): Retrieve Results of a finished Enrichment Analysis from miEAA

rba_mieaa_enrich_status(): Check Status of a Submitted Enrichment Analysis in miEAA

rba_mieaa_enrich_submit(): Submit miEAA miRNA Enrichment Analysis Request

PANTHER (rba_panther_*)

Functions that connect you to PANTHER (Protein Analysis THrough Evolutionary Relationships) API resources.

rba_panther_enrich(): PANTHER Over-Representation Enrichment Analysis

rba_panther_family(): Get PANTHER Families and Sub-Families

rba_panther_homolog(): Search PANTHER for Homologs of Gene(s)

rba_panther_info(): Get PANTHER database Information

rba_panther_mapping(): Map A Gene-set to PANTHER Database

rba_panther_ortholog(): Search PANTHER for Orthologs of Gene(s)

rba_panther_tree_grafter(): PANTHER Tree Grafter Use this function to retrieve a PANTHER family's tree topology information with a node corresponding to your sequence grafted in the best location in that tree.

Reactome Analysis Services (rba_reactome_*)

Functions that connect you to Reactome pathway database’s Analysis services API resources.

rba_reactome_analysis(): Reactome Over-Representation or Expression Analysis

rba_reactome_analysis_download(): Download Different Reactome Analysis Results

rba_reactome_analysis_import(): Import Saved Analysis JSON to Reactome

rba_reactome_analysis_mapping(): Maps Molecule Identifiers

rba_reactome_analysis_pdf(): Generate PDF file with Reactome Analysis Results

rba_reactome_analysis_species(): Compare Human Pathways with with Other Species

rba_reactome_analysis_token(): Return the Results Associated with a Token

Reactome Contents Services (rba_reactome_*)

Functions that connect you to Reactome pathway database’s Contents Services API resources.

Database Info Queries

rba_reactome_version(): The version number of current database

rba_reactome_diseases(): Reactome Diseases

Physical Entity Queries

rba_reactome_complex_list(): Get Complexes That Include a Molecule

rba_reactome_complex_subunits(): Get a Complex's Subunits

rba_reactome_participant_of(): Get Larger Reactome Structures Which Include an Entity

rba_reactome_entity_other_forms(): Get Other forms of a Reactome Entity

rba_reactome_event_ancestors(): Get Reactome Events Ancestors

rba_reactome_event_hierarchy(): Get Full Event Hierarchy of a Species

Format Exporter

rba_reactome_exporter_diagram(): Get a Reactome Event Diagram

rba_reactome_exporter_event(): Exports A Reactome Event to SBGN or SBML

rba_reactome_exporter_overview(): Get a Reactome Pathway Overview

rba_reactome_exporter_reaction(): Get a Reactome Reaction Event

Molecule Interactors

rba_reactome_interactors_psicquic(): The interface From Reactome to PSICQUIC

rba_reactome_interactors_static(): Get Static(IntAct) Interaction Information of a Protein

rba_reactome_mapping(): Map External ID to Reactome Pathways/Reactions

rba_reactome_orthology(): Get Orthologous (Computationally Inferred) Events

rba_reactome_participants(): Get Participants of a Reactome Event

rba_reactome_pathways_events(): Get Events Contained in an Upstream Events

rba_reactome_pathways_low(): Get lower level pathways Containing a 'Physical Entity' or Event

rba_reactome_pathways_top(): Get Top Level Pathways in a Species

Person Queries

rba_reactome_people_id(): A person by his identifiers

rba_reactome_people_name(): Get Persons Information by Name

Common Data Retrieval

rba_reactome_query(): Query and Retrieve any Reactome knowledge-base Object

ReferenceEntity Queries

rba_reactome_xref(): Map Cross References IDs to Reactome ReferenceEntity

rba_reactome_species(): Get Reactome Species

STRING (rba_string_*)

Functions that connect you to STRING (Functional protein association networks) API resources.

rba_string_annotations(): Retrieving Functional Annotation

rba_string_enrichment(): Getting Functional Enrichment

rba_string_enrichment_ppi(): Get Protein-Protein Interaction Enrichment

rba_string_homology_inter(): Get Similarity Scores Hits of Proteins in Different Species

rba_string_homology_intra(): Get Similarity Scores Hits of Proteins in a Species

rba_string_interaction_partners(): Get All STRING Interaction Partners

rba_string_interactions_network(): Get STRING Network Interactions

rba_string_map_ids(): Map a Set of Identifiers to STRING Identifiers

rba_string_network_image(): Get STRING Network Image

rba_string_version(): Get Current STRING Version

UniProt (rba_uniprot_*)

Functions that connect you to UniProt (Universal Protein Resource) API resources.

Coordinates

rba_uniprot_coordinates(): Get Genomic Coordinates of a Protein

rba_uniprot_coordinates_location(): Search UniProt entries by taxonomy and genomic coordinates

rba_uniprot_coordinates_search(): Search Genomic Coordinates of UniProt entries

rba_uniprot_coordinates_sequence(): Get Genome coordinate by Protein Sequence position

Proteins

rba_uniprot_proteins(): Get UniProt entry by accession

rba_uniprot_proteins_crossref(): Get UniProt Entry by UniProt Cross-Reference Database and ID

rba_uniprot_proteins_search(): Search UniProt entries

Features

rba_uniprot_features(): Get UniProt protein sequence features by accession

rba_uniprot_features_search(): UniProt maintains sequence annotations (features) that describe regions in the protein sequence. Using this function, you can search and retrieve UniProt proteins' sequence annotations (features). you may also refine your search query with variety of modifiers.

Variation

rba_uniprot_variation(): Get natural variants in UniProt by NIH-NCBI SNP database identifier

rba_uniprot_variation_search(): Search UniProt Natural Variants

Proteomics

rba_uniprot_proteomics(): Get Proteomics Peptides Mapped to UniProt Protein

rba_uniprot_proteomics_search(): Search Proteomics Peptides in UniProt

Post-Translational Modification (PTM)

rba_uniprot_ptm(): Get Post-Translational Modification of UniProt Protein

rba_uniprot_ptm_search(): Search Post-Translational Modification in UniProt

Antigens

rba_uniprot_antigens(): Get Antigens by UniProt Accession

rba_uniprot_antigens_search(): Search Antigens in UniProt

Mutagenesis

rba_uniprot_mutagenesis(): Get Mutagenesis by UniProt Accession

rba_uniprot_mutagenesis_search(): Search Mutagenesis in UniProt

Proteomes

rba_uniprot_proteomes(): Get proteome by proteome/proteins UPID

rba_uniprot_proteomes_search(): Search Proteomes in UniProt

rba_uniprot_genecentric(): Get Gene-Centric proteins by UniProt Accession

rba_uniprot_genecentric_search(): Search Gene-Centric Proteins

Taxonomy

rba_uniprot_taxonomy(): Get UniProt Taxonomy Nodes

rba_uniprot_taxonomy_lca(): Get Lowest Common Ancestor (LCA) of Two Taxonomy Nodes

rba_uniprot_taxonomy_lineage(): Get Taxonomic Lineage

rba_uniprot_taxonomy_name(): Search UniProt Taxonomic Names

rba_uniprot_taxonomy_path(): Traverse UniProt Taxonomic Tree Path

rba_uniprot_taxonomy_relationship(): Get Shortest Path Between Two Taxonomy Nodes

UniParc

rba_uniprot_uniparc(): Get UniParc entry

rba_uniprot_uniparc_bestguess(): Get UniParc Longest Sequence for Entries

rba_uniprot_uniparc_search(): Search UniParc Entries

rba_uniprot_uniparc_sequence(): Get UniParc Entries by Sequence