# User-Friendly R Interface to Biologic Web Services' API

## Documentation for package ‘rbioapi’ version 0.8.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

R

## -- R --

rba_connection_test | Test if the Supported Services Are Responding
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
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
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 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
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_participants | Get Participants of a Reactome Event
rba_reactome_participant_of | Get Larger Reactome Structures Which Include an Entity
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_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_interactions_network | Get STRING Network Interactions
rba_string_interaction_partners | Get All STRING Interaction Partners
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_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
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_genecentric | Get Gene-Centric proteins by UniProt Accession
rba_uniprot_genecentric_search | Search Gene-Centric Proteins
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_proteomes | Get proteome by proteome/proteins UPID
rba_uniprot_proteomes_search | Search Proteomes in UniProt
rba_uniprot_proteomics | Get Proteomics Peptides Mapped to UniProt Protein (Deprecated)
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_search | Search Proteomics Peptides in UniProt (Deprecated)
rba_uniprot_proteomics_species | Get UniProt Proteomics Metadata
rba_uniprot_ptm | Get Post-Translational Modification of UniProt Protein (Deprecated)
rba_uniprot_ptm_search | Search Post-Translational Modification in UniProt (Deprecated)
rba_uniprot_rna_edit | Retrieve Epitope by Accession
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_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
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
rba_uniprot_variation | Get natural variants in UniProt by NIH-NCBI SNP database identifier
rba_uniprot_variation_search | Search UniProt Natural Variants