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rbioapi (version 0.8.2)

User-Friendly R Interface to Biologic Web Services' API

Description

Currently fully supports Enrichr, JASPAR, miEAA, PANTHER, Reactome, STRING, and UniProt! The goal of rbioapi is to provide a user-friendly and consistent interface to biological databases and services. In a way that insulates the user from the technicalities of using web services API and creates a unified and easy-to-use interface to biological and medical web services. This is an ongoing project; New databases and services will be added periodically. Feel free to suggest any databases or services you often use.

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Version

Install

install.packages('rbioapi')

Monthly Downloads

353

Version

0.8.2

License

GPL-3

Issues

0

Pull Requests

0

Stars

22

Forks

1

Maintainer

Moosa Rezwani

Last Published

February 7th, 2025

Functions in rbioapi (0.8.2)

rba_jaspar_collections_matrices

List matrices available in a JASPAR collection
rba_enrichr_add_list

Upload Your Gene-List to Enrichr
rba_enrichr

A One-step Wrapper for Gene-list Enrichment Using Enrichr
rba_enrichr_view_list

View an Uploaded Gene List
rba_connection_test

Test if the Supported Services Are Responding
rba_enrichr_gene_map

Find Enrichr Terms That Contain a Given Gene
rba_enrichr_enrich

Get Enrichr Enrichment Results
rba_jaspar_collections

List collections available in JASPAR
rba_enrichr_libs

Retrieve a List of available libraries from Enrichr
rba_enrichr_add_background

Upload Background Gene-List to Enrichr
rba_jaspar_matrix_versions

List matrix profile versions associated with a base ID
rba_jaspar_taxons

List available taxonomic groups in JASPAR
rba_jaspar_species_matrices

List matrices available in JASPAR of a species
rba_jaspar_matrix

Get a Position Frequency Matrices (PFM) with annotations
rba_jaspar_tffm

Get a TF flexible models (TFFMs) information
rba_jaspar_taxons_matrices

List matrices available in JASPAR of a taxonomic group
rba_jaspar_releases

Get information about JASPAR database releases
rba_jaspar_sites

Get binding sites of a matrix profile
rba_jaspar_matrix_search

Search matrix profiles available in JASPAR
rba_jaspar_species

List available species in JASPAR
rba_mieaa_convert_type

Convert Between Mature and precursor miRNA Accession
rba_mieaa_enrich_status

Check Status of a Submitted Enrichment Analysis in miEAA
rba_mieaa_convert_version

Convert miRNA accession Between Different miRBase Versions
rba_mieaa_enrich_submit

Submit miEAA miRNA Enrichment Analysis Request
rba_mieaa_enrich_results

Retrieve Results of a finished Enrichment Analysis from miEAA
rba_mieaa_enrich

A One-step Wrapper for miRNA Enrichment Using miEAA
rba_jaspar_tffm_search

Search TF flexible models (TFFMs) available in JASPAR
rba_mieaa_cats

Get Supported Enrichment Categories for a Species and miRNA Type
rba_options

Set rbioapi Global Options
rba_pages

Get Multiple Pages of a Paginated Resource
rba_panther_info

Get PANTHER database Information
rba_panther_homolog

Search PANTHER for Homologs of Gene(s)
rba_panther_enrich

PANTHER Over-Representation or Enrichment Analysis
rba_panther_ortholog

Search PANTHER for Orthologs of Gene(s)
rba_panther_mapping

Map A Gene-set to PANTHER Database
rba_panther_family

Get PANTHER Families and Sub-Families
rba_reactome_analysis_download

Download Different Reactome Analysis Results
rba_reactome_analysis_import

Import Saved Analysis JSON to Reactome
rba_panther_tree_grafter

PANTHER Tree Grafter
rba_reactome_analysis_species

Compare Human Pathways with with Other Species
rba_reactome_diseases

Reactome Diseases
rba_reactome_analysis

Reactome Over-Representation or Expression Analysis
rba_reactome_event_ancestors

Get Reactome Events Ancestors
rba_reactome_event_hierarchy

Get Full Event Hierarchy of a Species
rba_reactome_analysis_pdf

Generate PDF file with Reactome Analysis Results
rba_reactome_analysis_mapping

Maps Molecule Identifiers
rba_reactome_entity_other_forms

Get Other forms of a Reactome Entity
rba_reactome_complex_subunits

Get a Complex's Subunits
rba_reactome_complex_list

Get Complexes That Include a Molecule
rba_reactome_exporter_event

Exports A Reactome Event to SBGN or SBML
rba_reactome_mapping

Map External ID to Reactome Pathways/Reactions
rba_reactome_exporter_diagram

Get a Reactome Event Diagram
rba_reactome_orthology

Get Orthologous (Computationally Inferred) Events
rba_reactome_participants

Get Participants of a Reactome Event
rba_reactome_participant_of

Get Larger Reactome Structures Which Include an Entity
rba_reactome_interactors_static

Get Static(IntAct) Interaction Information of a Protein
rba_reactome_interactors_psicquic

The interface From Reactome to PSICQUIC
rba_reactome_analysis_token

Return the Results Associated with a Token
rba_reactome_exporter_reaction

Get a Reactome Reaction Event
rba_reactome_exporter_overview

Get a Reactome Pathway Overview
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_version

The version number of current database
rba_reactome_species

Get Reactome Species
rba_reactome_query

Query and Retrieve any Reactome knowledge-base Object
rba_reactome_people_name

Get Persons Information by Name
rba_string_annotations

Retrieving Functional Annotation
rba_string_enrichment

Getting Functional Enrichment
rba_string_enrichment_ppi

Get Protein-Protein Interaction Enrichment
rba_reactome_xref

Map Cross References IDs to Reactome ReferenceEntity
rba_string_interactions_network

Get STRING Network Interactions
rba_string_homology_inter

Get Similarity Scores Hits of Proteins in Different Species
rba_string_enrichment_image

Get STRING Enrichment Plot
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_string_homology_intra

Get Similarity Scores Hits of Proteins in a Species
rba_uniprot_epitope_search

Search UniProt Epitopes
rba_uniprot_coordinates_location

Search UniProt entries by taxonomy and genomic coordinates
rba_uniprot_coordinates_search

Search Genomic Coordinates of UniProt entries
rba_uniprot_antigens

Get Antigens by UniProt Accession
rba_uniprot_coordinates

Get Genomic Coordinates of a Protein
rba_string_interaction_partners

Get All STRING Interaction Partners
rba_uniprot_coordinates_location_genome

Get Genome coordinate by Gene Sequence position
rba_uniprot_antigens_search

Search Antigens in UniProt
rba_uniprot_proteins_crossref

Get UniProt Entry by UniProt Cross-Reference Database and ID
rba_uniprot_proteins_search

Search UniProt entries
rba_uniprot_genecentric_search

Search Gene-Centric Proteins
rba_uniprot_mutagenesis

Get Mutagenesis by UniProt Accession
rba_uniprot_features

Get UniProt protein sequence features by accession
rba_uniprot_features_search

Search UniProt protein sequence features
rba_uniprot_genecentric

Get Gene-Centric proteins by UniProt Accession
rba_uniprot_proteins

Get UniProt entry by accession
rba_uniprot_epitope

Retrieve Epitopes by Accession
rba_uniprot_mutagenesis_search

Search Mutagenesis in UniProt
rba_uniprot_proteomics_ptm_search

Search Post-Translational Modification Proteomics in UniProt
rba_uniprot_proteomics_hpp_search

Search HPP Proteomics data in UniProt
rba_uniprot_proteomics_search

Search Proteomics Peptides in UniProt (Deprecated)
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_coordinates_location_protein

Get Genome coordinate by Protein Sequence position
rba_uniprot_proteomes_search

Search Proteomes in UniProt
rba_uniprot_proteomes

Get proteome by proteome/proteins UPID
rba_uniprot_proteomics

Get Proteomics Peptides Mapped to UniProt Protein (Deprecated)
rba_uniprot_proteomics_hpp

Get HPP Proteomics data in UniProt
rba_uniprot_ptm

Get Post-Translational Modification of UniProt Protein (Deprecated)
rba_uniprot_proteomics_species

Get UniProt Proteomics Metadata
rba_uniprot_rna_edit_search

Search RNA Editing in UniProt
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_uniparc

Get UniParc entry
rba_uniprot_taxonomy_relationship

Get Shortest Path Between Two Taxonomy Nodes
rba_uniprot_taxonomy_name

Search UniProt Taxonomic Names
rba_uniprot_taxonomy_path

Traverse UniProt Taxonomic Tree Path
rba_uniprot_variation

Get natural variants in UniProt by NIH-NCBI SNP database identifier
rba_uniprot_uniparc_sequence

Get UniParc Entries by Sequence
rba_uniprot_rna_edit

Retrieve Epitope by Accession
rba_uniprot_ptm_search

Search Post-Translational Modification in UniProt (Deprecated)
rba_uniprot_uniparc_bestguess

Get UniParc Longest Sequence for Entries
rba_uniprot_uniparc_search

Search UniParc Entries
rba_uniprot_variation_search

Search UniProt Natural Variants
rbioapi

rbioapi: User-Friendly R Interface to Biologic Web Services' API