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Helper functions

These function serve as helpers to the overall exprerince 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 miEAA (miRNA Enrichment Analysis and Annotation 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 (a database of curated 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 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 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 (PPI database) 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