User-Friendly R Interface to Biologic Web Services' API


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Documentation for package ‘rbioapi’ version 0.8.2

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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