Package index

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_background(): Upload Background Gene-List to 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 or 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_image(): Get STRING Enrichment Plot

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.

Proteins - Proteins

rba_uniprot_antigens(): Get Antigens by UniProt Accession

rba_uniprot_antigens_search(): Search Antigens in UniProt

rba_uniprot_epitope(): Retrieve Epitopes by Accession

rba_uniprot_epitope_search(): Search UniProt Epitopes

rba_uniprot_features(): Get UniProt protein sequence features by accession

rba_uniprot_features_search(): Search UniProt protein sequence features

rba_uniprot_mutagenesis(): Get Mutagenesis by UniProt Accession

rba_uniprot_mutagenesis_search(): Search Mutagenesis in UniProt

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

rba_uniprot_rna_edit(): Retrieve Epitope by Accession

rba_uniprot_rna_edit_search(): Search RNA Editing in UniProt

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_hpp(): Get HPP Proteomics data in UniProt

rba_uniprot_proteomics_hpp_search(): Search HPP Proteomics data in UniProt

rba_uniprot_proteomics_non_ptm(): Get Proteomics data in UniProt

rba_uniprot_proteomics_non_ptm_search(): Search Proteomics data in UniProt

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

rba_uniprot_proteomics_ptm_search(): Search Post-Translational Modification Proteomics in UniProt

rba_uniprot_proteomics_species(): Get UniProt Proteomics Metadata

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

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_location_genome(): Get Genome coordinate by Gene Sequence position

rba_uniprot_coordinates_location_protein(): Get Genome coordinate by Protein Sequence position

rba_uniprot_coordinates_search(): Search Genomic Coordinates of UniProt entries

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