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rbioapi

User-Friendly R Interface to Biologic Web Services' API

Currently fully supports miEAA, PANTHER, Reactome, STRING, and UniProt! The goal of rbioapi is to provide a user-friendly and consistent interface to biological databases and services; It is designed in a way that insulates the user from technicalities when it comes to using API services and creates a unified and easy-to-implement tool to connect to biological databases and services. With rbioapi, You are not required to have any prior technical knowledge. Just fill in a function's arguments and the rest is handled for you. This an ongoing project. New databases and services will be implemented periodically to gradually make rbioapi more comprehensive. Feel free to suggest any databases or services you often use.

Functions (89)

rba_connection_test

Test if the Supported Services Are Responding

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

rba_options

Set rbioapi Global Options

rba_pages

Get Multiple Pages of a Paginated Resource

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.

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

rba_reactome_complex_list

Get Complexes That Include a Molecule

rba_reactome_complex_subunits

Get a Complex's Subunits

rba_reactome_diseases

Reactome Diseases

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

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

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_participant_of

Get Larger Reactome Structures Which Include an Entity

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

rba_reactome_people_id

A person by his identifiers

rba_reactome_people_name

Get Persons Information by Name

rba_reactome_query

Query and Retrieve any Reactome knowledge-base Object

rba_reactome_species

Get Reactome Species

rba_reactome_version

The version number of current database

rba_reactome_xref

Map Cross References IDs to Reactome ReferenceEntity

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

rba_uniprot_antigens

Get Antigens by UniProt Accession

rba_uniprot_antigens_search

Search Antigens in UniProt

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

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.

rba_uniprot_genecentric

Get Gene-Centric proteins by UniProt Accession

rba_uniprot_genecentric_search

Search Gene-Centric 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

rba_uniprot_proteomes

Get proteome by proteome/proteins UPID