{ "_id": "6a1544a5acfb0bcc41d56d92", "Type": "Package", "Package": "rbioapi", "Title": "User-Friendly R Interface to Biologic Web Services' API", "Version": "0.8.3", "Authors@R": "person(given = \"Moosa\",\nfamily = \"Rezwani\",\nrole = c(\"aut\", \"cre\"),\nemail = \"moosa.rezwani@gmail.com\",\ncomment = c(ORCID = \"0000-0001-6325-4444\")\n)", "Description": "Currently fully supports Enrichr, JASPAR, miEAA, PANTHER,\nReactome, STRING, and UniProt! The goal of rbioapi is to\nprovide a user-friendly and consistent interface to biological\ndatabases and services. In a way that insulates the user from\nthe technicalities of using web services API and creates a\nunified and easy-to-use interface to biological and medical web\nservices. This is an ongoing project; New databases and\nservices will be added periodically. Feel free to suggest any\ndatabases or services you often use.", "License": "GPL-3", "URL": "https://rbioapi.moosa-r.com, https://github.com/moosa-r/rbioapi", "BugReports": "https://github.com/moosa-r/rbioapi/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://moosa-r.r-universe.dev", "Date/Publication": "2026-01-26 12:52:05 UTC", "RemoteUrl": "https://github.com/moosa-r/rbioapi", "RemoteRef": "HEAD", "RemoteSha": "35c26b5f4f320ade12ec67a2b6802e129aabfbd6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 06:55:02 UTC", "User": "root" }, "Author": "Moosa Rezwani [aut, cre] (ORCID:\n)", "Maintainer": "Moosa Rezwani ", "MD5sum": "93952bddec64b6cae8305e9d9b21a071", "_user": "moosa-r", "_type": "src", "_file": "rbioapi_0.8.3.tar.gz", "_fileid": "604b001c58c3b5bfc6f15eb718328f9f1d432764906780f9ef50d3bcf16e9edc", "_filesize": 1800599, "_sha256": 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"_devurl": "https://github.com/moosa-r/rbioapi", "_pkgdown": "https://rbioapi.moosa-r.com", "_searchresults": 84, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/rbioapi.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/moosa-r/rbioapi", "_realowner": "moosa-r", "_cranurl": true, "_releases": [ { "version": "0.7.0", "date": "2021-04-30" }, { "version": "0.7.4", "date": "2021-06-22" }, { "version": "0.7.6", "date": "2022-04-05" }, { "version": "0.7.7", "date": "2022-08-08" }, { "version": "0.7.8", "date": "2023-05-02" }, { "version": "0.7.9", "date": "2023-05-10" }, { "version": "0.8.0", "date": "2023-09-30" }, { "version": "0.8.1", "date": "2024-03-30" }, { "version": "0.8.2", "date": "2025-02-07" }, { "version": "0.8.3", "date": "2025-07-03" } ], "_exports": [ "rba_connection_test", "rba_enrichr", "rba_enrichr_add_background", "rba_enrichr_add_list", "rba_enrichr_enrich", "rba_enrichr_gene_map", "rba_enrichr_libs", "rba_enrichr_view_list", "rba_jaspar_collections", "rba_jaspar_collections_matrices", "rba_jaspar_matrix", "rba_jaspar_matrix_search", "rba_jaspar_matrix_versions", "rba_jaspar_releases", "rba_jaspar_sites", "rba_jaspar_species", "rba_jaspar_species_matrices", "rba_jaspar_taxons", "rba_jaspar_taxons_matrices", "rba_jaspar_tffm", "rba_jaspar_tffm_search", "rba_mieaa_cats", "rba_mieaa_convert_type", "rba_mieaa_convert_version", "rba_mieaa_enrich", "rba_mieaa_enrich_results", "rba_mieaa_enrich_status", "rba_mieaa_enrich_submit", "rba_options", "rba_pages", "rba_panther_enrich", "rba_panther_family", "rba_panther_homolog", "rba_panther_info", "rba_panther_mapping", "rba_panther_ortholog", "rba_panther_tree_grafter", "rba_reactome_analysis", "rba_reactome_analysis_download", "rba_reactome_analysis_import", "rba_reactome_analysis_mapping", "rba_reactome_analysis_pdf", "rba_reactome_analysis_species", "rba_reactome_analysis_token", "rba_reactome_complex_list", "rba_reactome_complex_subunits", "rba_reactome_diseases", "rba_reactome_entity_other_forms", "rba_reactome_event_ancestors", "rba_reactome_event_hierarchy", "rba_reactome_exporter_diagram", "rba_reactome_exporter_event", "rba_reactome_exporter_overview", "rba_reactome_exporter_reaction", "rba_reactome_interactors_psicquic", "rba_reactome_interactors_static", "rba_reactome_mapping", "rba_reactome_orthology", "rba_reactome_participant_of", "rba_reactome_participants", "rba_reactome_pathways_events", "rba_reactome_pathways_low", "rba_reactome_pathways_top", "rba_reactome_people_id", "rba_reactome_people_name", "rba_reactome_query", "rba_reactome_species", "rba_reactome_version", "rba_reactome_xref", "rba_string_annotations", "rba_string_enrichment", "rba_string_enrichment_image", "rba_string_enrichment_ppi", "rba_string_homology_inter", "rba_string_homology_intra", "rba_string_interaction_partners", "rba_string_interactions_network", "rba_string_map_ids", "rba_string_network_image", "rba_string_version", "rba_uniprot_antigens", "rba_uniprot_antigens_search", "rba_uniprot_coordinates", "rba_uniprot_coordinates_location", "rba_uniprot_coordinates_location_genome", "rba_uniprot_coordinates_location_protein", "rba_uniprot_coordinates_search", "rba_uniprot_epitope", "rba_uniprot_epitope_search", "rba_uniprot_features", "rba_uniprot_features_search", "rba_uniprot_genecentric", "rba_uniprot_genecentric_search", "rba_uniprot_mutagenesis", "rba_uniprot_mutagenesis_search", "rba_uniprot_proteins", "rba_uniprot_proteins_crossref", "rba_uniprot_proteins_search", "rba_uniprot_proteomes", "rba_uniprot_proteomes_search", "rba_uniprot_proteomics", "rba_uniprot_proteomics_hpp", "rba_uniprot_proteomics_hpp_search", "rba_uniprot_proteomics_non_ptm", "rba_uniprot_proteomics_non_ptm_search", "rba_uniprot_proteomics_ptm", "rba_uniprot_proteomics_ptm_search", "rba_uniprot_proteomics_search", "rba_uniprot_proteomics_species", "rba_uniprot_ptm", "rba_uniprot_ptm_search", "rba_uniprot_rna_edit", "rba_uniprot_rna_edit_search", "rba_uniprot_taxonomy", "rba_uniprot_taxonomy_lca", "rba_uniprot_taxonomy_lineage", "rba_uniprot_taxonomy_name", "rba_uniprot_taxonomy_path", "rba_uniprot_taxonomy_relationship", "rba_uniprot_uniparc", "rba_uniprot_uniparc_bestguess", "rba_uniprot_uniparc_search", "rba_uniprot_uniparc_sequence", "rba_uniprot_variation", "rba_uniprot_variation_search" ], "_help": [ { "page": "rba_connection_test", "title": "Test if the Supported Services Are Responding", "concept": [ "\"Helper functions\"" ], "topics": [ "rba_connection_test" ] }, { "page": "rba_enrichr", "title": "A One-step Wrapper for Gene-list Enrichment Using Enrichr", "concept": [ "\"Enrichment/Over-representation\"", "\"Enrichr\"" ], "topics": [ "rba_enrichr" ] }, { "page": "rba_enrichr_add_background", "title": "Upload Background Gene-List to Enrichr", "concept": [ "\"Enrichr\"" ], "topics": [ "rba_enrichr_add_background" ] }, { "page": "rba_enrichr_add_list", "title": "Upload Your Gene-List to Enrichr", "concept": [ "\"Enrichr\"" ], "topics": [ "rba_enrichr_add_list" ] }, { "page": "rba_enrichr_enrich", "title": "Get Enrichr Enrichment Results", "concept": [ "\"Enrichr\"" ], "topics": [ "rba_enrichr_enrich" ] }, { "page": "rba_enrichr_gene_map", "title": "Find Enrichr Terms That Contain a Given Gene", "concept": [ "\"Enrichr\"" ], "topics": [ "rba_enrichr_gene_map" ] }, { "page": "rba_enrichr_libs", "title": "Retrieve a List of available libraries from Enrichr", "concept": [ "\"Enrichr\"" ], "topics": [ "rba_enrichr_libs" ] }, { "page": "rba_enrichr_view_list", "title": "View an Uploaded Gene List", "concept": [ "\"Enrichr\"" ], "topics": [ "rba_enrichr_view_list" ] }, { "page": "rba_jaspar_collections", "title": "List collections available in JASPAR", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_collections" ] }, { "page": "rba_jaspar_collections_matrices", "title": "List matrices available in a JASPAR collection", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_collections_matrices" ] }, { "page": "rba_jaspar_matrix", "title": "Get a Position Frequency Matrices (PFM) with annotations", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_matrix" ] }, { "page": "rba_jaspar_matrix_search", "title": "Search matrix profiles available in JASPAR", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_matrix_search" ] }, { "page": "rba_jaspar_matrix_versions", "title": "List matrix profile versions associated with a base ID", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_matrix_versions" ] }, { "page": "rba_jaspar_releases", "title": "Get information about JASPAR database releases", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_releases" ] }, { "page": "rba_jaspar_sites", "title": "Get binding sites of a matrix profile", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_sites" ] }, { "page": "rba_jaspar_species", "title": "List available species in JASPAR", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_species" ] }, { "page": "rba_jaspar_species_matrices", "title": "List matrices available in JASPAR of a species", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_species_matrices" ] }, { "page": "rba_jaspar_taxons", "title": "List available taxonomic groups in JASPAR", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_taxons" ] }, { "page": "rba_jaspar_taxons_matrices", "title": "List matrices available in JASPAR of a taxonomic group", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_taxons_matrices" ] }, { "page": "rba_jaspar_tffm", "title": "Get a TF flexible models (TFFMs) information", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_tffm" ] }, { "page": "rba_jaspar_tffm_search", "title": "Search TF flexible models (TFFMs) available in JASPAR", "concept": [ "\"JASPAR\"" ], "topics": [ "rba_jaspar_tffm_search" ] }, { "page": "rba_mieaa_cats", "title": "Get Supported Enrichment Categories for a Species and miRNA Type", "concept": [ "\"miEAA\"" ], "topics": [ "rba_mieaa_cats" ] }, { "page": "rba_mieaa_convert_type", "title": "Convert Between Mature and precursor miRNA Accession", "concept": [ "\"miEAA\"" ], "topics": [ "rba_mieaa_convert_type" ] }, { "page": "rba_mieaa_convert_version", "title": "Convert miRNA accession Between Different miRBase Versions", "concept": [ "\"miEAA\"" ], "topics": [ "rba_mieaa_convert_version" ] }, { "page": "rba_mieaa_enrich", "title": "A One-step Wrapper for miRNA Enrichment Using miEAA", "concept": [ "\"Enrichment/Over-representation\"", "\"miEAA\"" ], "topics": [ "rba_mieaa_enrich" ] }, { "page": "rba_mieaa_enrich_results", "title": "Retrieve Results of a finished Enrichment Analysis from miEAA", "concept": [ "\"miEAA\"" ], "topics": [ "rba_mieaa_enrich_results" ] }, { "page": "rba_mieaa_enrich_status", "title": "Check Status of a Submitted Enrichment Analysis in miEAA", "concept": [ "\"miEAA\"" ], "topics": [ "rba_mieaa_enrich_status" ] }, { "page": "rba_mieaa_enrich_submit", "title": "Submit miEAA miRNA Enrichment Analysis Request", "concept": [ "\"miEAA\"" ], "topics": [ "rba_mieaa_enrich_submit" ] }, { "page": "rba_options", "title": "Set rbioapi Global Options", "concept": [ "\"Helper functions\"" ], "topics": [ "rba_options" ] }, { "page": "rba_pages", "title": "Get Multiple Pages of a Paginated Resource", "concept": [ "\"Helper functions\"" ], "topics": [ "rba_pages" ] }, { "page": "rba_panther_enrich", "title": "PANTHER Over-Representation or Enrichment Analysis", "concept": [ "\"Enrichment/Over-representation\"", "\"PANTHER\"" ], "topics": [ "rba_panther_enrich" ] }, { "page": "rba_panther_family", "title": "Get PANTHER Families and Sub-Families", "concept": [ "\"PANTHER\"" ], "topics": [ "rba_panther_family" ] }, { "page": "rba_panther_homolog", "title": "Search PANTHER for Homologs of Gene(s)", "concept": [ "\"PANTHER\"" ], "topics": [ "rba_panther_homolog" ] }, { "page": "rba_panther_info", "title": "Get PANTHER database Information", "concept": [ "\"PANTHER\"" ], "topics": [ "rba_panther_info" ] }, { "page": "rba_panther_mapping", "title": "Map A Gene-set to PANTHER Database", "concept": [ "\"PANTHER\"" ], "topics": [ "rba_panther_mapping" ] }, { "page": "rba_panther_ortholog", "title": "Search PANTHER for Orthologs of Gene(s)", "concept": [ "\"PANTHER\"" ], "topics": [ "rba_panther_ortholog" ] }, { "page": "rba_panther_tree_grafter", "title": "PANTHER Tree Grafter", "concept": [ "\"PANTHER\"" ], "topics": [ "rba_panther_tree_grafter" ] }, { "page": "rba_reactome_analysis", "title": "Reactome Over-Representation or Expression Analysis", "concept": [ "\"Enrichment/Over-representation\"", "\"Reactome Analysis Service\"" ], "topics": [ "rba_reactome_analysis" ] }, { "page": "rba_reactome_analysis_download", "title": "Download Different Reactome Analysis Results", "concept": [ "\"Reactome Analysis Service\"" ], "topics": [ "rba_reactome_analysis_download" ] }, { "page": "rba_reactome_analysis_import", "title": "Import Saved Analysis JSON to Reactome", "concept": [ "\"Reactome Analysis Service\"" ], "topics": [ "rba_reactome_analysis_import" ] }, { "page": "rba_reactome_analysis_mapping", "title": "Maps Molecule Identifiers", "concept": [ "\"Reactome Analysis Service\"" ], "topics": [ "rba_reactome_analysis_mapping" ] }, { "page": "rba_reactome_analysis_pdf", "title": "Generate PDF file with Reactome Analysis Results", "concept": [ "\"Reactome Analysis Service\"" ], "topics": [ "rba_reactome_analysis_pdf" ] }, { "page": "rba_reactome_analysis_species", "title": "Compare Human Pathways with with Other Species", "concept": [ "\"Reactome Analysis Service\"" ], "topics": [ "rba_reactome_analysis_species" ] }, { "page": "rba_reactome_analysis_token", "title": "Return the Results Associated with a Token", "concept": [ "\"Reactome Analysis Service\"" ], "topics": [ "rba_reactome_analysis_token" ] }, { "page": "rba_reactome_complex_list", "title": "Get Complexes That Include a Molecule", "concept": [ "\"Reactome Content Service - Physical Entity Queries\"" ], "topics": [ "rba_reactome_complex_list" ] }, { "page": "rba_reactome_complex_subunits", "title": "Get a Complex's Subunits", "concept": [ "\"Reactome Content Service - Physical Entity Queries\"" ], "topics": [ "rba_reactome_complex_subunits" ] }, { "page": "rba_reactome_diseases", "title": "Reactome Diseases", "concept": [ "\"Reactome Content Service - Disease Related Queries\"" ], "topics": [ "rba_reactome_diseases" ] }, { "page": "rba_reactome_entity_other_forms", "title": "Get Other forms of a Reactome Entity", "concept": [ "\"Reactome Content Service - Physical Entity Queries\"" ], "topics": [ "rba_reactome_entity_other_forms" ] }, { "page": "rba_reactome_event_ancestors", "title": "Get Reactome Events Ancestors", "concept": [ "\"Reactome Content Service - Queries Related to Events\"" ], "topics": [ "rba_reactome_event_ancestors" ] }, { "page": "rba_reactome_event_hierarchy", "title": "Get Full Event Hierarchy of a Species", "concept": [ "\"Reactome Content Service - Queries Related to Events\"" ], "topics": [ "rba_reactome_event_hierarchy" ] }, { "page": "rba_reactome_exporter_diagram", "title": "Get a Reactome Event Diagram", "concept": [ "\"Reactome Content Service - Format Exporter\"" ], "topics": [ "rba_reactome_exporter_diagram" ] }, { "page": "rba_reactome_exporter_event", "title": "Exports A Reactome Event to SBGN or SBML", "concept": [ "\"Reactome Content Service - Format Exporter\"" ], "topics": [ "rba_reactome_exporter_event" ] }, { "page": "rba_reactome_exporter_overview", "title": "Get a Reactome Pathway Overview", "concept": [ "\"Reactome Content Service - Format Exporter\"" ], "topics": [ "rba_reactome_exporter_overview" ] }, { "page": "rba_reactome_exporter_reaction", "title": "Get a Reactome Reaction Event", "concept": [ "\"Reactome Content Service - Format Exporter\"" ], "topics": [ "rba_reactome_exporter_reaction" ] }, { "page": "rba_reactome_interactors_psicquic", "title": "The interface From Reactome to PSICQUIC", "concept": [ "\"Reactome Content Service - Molecule Interactors\"" ], "topics": [ "rba_reactome_interactors_psicquic" ] }, { "page": "rba_reactome_interactors_static", "title": "Get Static(IntAct) Interaction Information of a Protein", "concept": [ "\"Reactome Content Service - Molecule Interactors\"" ], "topics": [ "rba_reactome_interactors_static" ] }, { "page": "rba_reactome_mapping", "title": "Map External ID to Reactome Pathways/Reactions", "concept": [ "\"Reactome Content Service - Mapping Related Queries\"" ], "topics": [ "rba_reactome_mapping" ] }, { "page": "rba_reactome_orthology", "title": "Get Orthologous (Computationally Inferred) Events", "concept": [ "\"Reactome Content Service - Orthology Related Queries\"" ], "topics": [ "rba_reactome_orthology" ] }, { "page": "rba_reactome_participant_of", "title": "Get Larger Reactome Structures Which Include an Entity", "concept": [ "\"Reactome Content Service - Physical Entity Queries\"" ], "topics": [ "rba_reactome_participant_of" ] }, { "page": "rba_reactome_participants", "title": "Get Participants of a Reactome Event", "concept": [ "\"Reactome Content Service - Queries Related to Participants\"" ], "topics": [ "rba_reactome_participants" ] }, { "page": "rba_reactome_pathways_events", "title": "Get Events Contained in an Upstream Events", "concept": [ "\"Reactome Content Service - Pathway Related Queries\"" ], "topics": [ "rba_reactome_pathways_events" ] }, { "page": "rba_reactome_pathways_low", "title": "Get lower level pathways Containing a 'Physical Entity' or Event", "concept": [ "\"Reactome Content Service - Pathway Related Queries\"" ], "topics": [ "rba_reactome_pathways_low" ] }, { "page": "rba_reactome_pathways_top", "title": "Get Top Level Pathways in a Species", "concept": [ "\"Reactome Content Service - Pathway Related Queries\"" ], "topics": [ "rba_reactome_pathways_top" ] }, { "page": "rba_reactome_people_id", "title": "A person by his identifiers", "concept": [ "\"Reactome Content Service - Person Queries\"" ], "topics": [ "rba_reactome_people_id" ] }, { "page": "rba_reactome_people_name", "title": "Get Persons Information by Name", "concept": [ "\"Reactome Content Service - Person Queries\"" ], "topics": [ "rba_reactome_people_name" ] }, { "page": "rba_reactome_query", "title": "Query and Retrieve any Reactome knowledge-base Object", "concept": [ "\"Reactome Content Service - Common Data Retrieval\"" ], "topics": [ "rba_reactome_query" ] }, { "page": "rba_reactome_species", "title": "Get Reactome Species", "concept": [ "\"Reactome Content Service - Species Related Queries\"" ], "topics": [ "rba_reactome_species" ] }, { "page": "rba_reactome_version", "title": "The version number of current database", "concept": [ "\"Reactome Content Service - Database Info Queries\"" ], "topics": [ "rba_reactome_version" ] }, { "page": "rba_reactome_xref", "title": "Map Cross References IDs to Reactome ReferenceEntity", "concept": [ "\"Reactome Content Service - ReferenceEntity Queries\"" ], "topics": [ "rba_reactome_xref" ] }, { "page": "rba_string_annotations", "title": "Retrieving Functional Annotation", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_annotations" ] }, { "page": "rba_string_enrichment", "title": "Getting Functional Enrichment", "concept": [ "\"Enrichment/Over-representation\"", "\"STRING\"" ], "topics": [ "rba_string_enrichment" ] }, { "page": "rba_string_enrichment_image", "title": "Get STRING Enrichment Plot", "concept": [ "\"Enrichment/Over-representation\"", "\"STRING\"" ], "topics": [ "rba_string_enrichment_image" ] }, { "page": "rba_string_enrichment_ppi", "title": "Get Protein-Protein Interaction Enrichment", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_enrichment_ppi" ] }, { "page": "rba_string_homology_inter", "title": "Get Similarity Scores Hits of Proteins in Different Species", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_homology_inter" ] }, { "page": "rba_string_homology_intra", "title": "Get Similarity Scores Hits of Proteins in a Species", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_homology_intra" ] }, { "page": "rba_string_interaction_partners", "title": "Get All STRING Interaction Partners", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_interaction_partners" ] }, { "page": "rba_string_interactions_network", "title": "Get STRING Network Interactions", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_interactions_network" ] }, { "page": "rba_string_map_ids", "title": "Map a Set of Identifiers to STRING Identifiers", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_map_ids" ] }, { "page": "rba_string_network_image", "title": "Get STRING Network Image", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_network_image" ] }, { "page": "rba_string_version", "title": "Get Current STRING Version", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_version" ] }, { "page": "rba_uniprot_antigens", "title": "Get Antigens by UniProt Accession", "concept": [ "\"UniProt - Antigen\"" ], "topics": [ "rba_uniprot_antigens" ] }, { "page": "rba_uniprot_antigens_search", "title": "Search Antigens in UniProt", "concept": [ "\"UniProt - Antigen\"" ], "topics": [ "rba_uniprot_antigens_search" ] }, { "page": "rba_uniprot_coordinates", "title": "Get Genomic Coordinates of a Protein", "concept": [ "\"UniProt - Coordinates\"" ], "topics": [ "rba_uniprot_coordinates" ] }, { "page": "rba_uniprot_coordinates_location", "title": "Search UniProt entries by taxonomy and genomic coordinates", "concept": [ "\"UniProt - Coordinates\"" ], "topics": [ "rba_uniprot_coordinates_location" ] }, { "page": "rba_uniprot_coordinates_location_genome", "title": "Get Genome coordinate by Gene Sequence position", "concept": [ "\"UniProt - Coordinates\"" ], "topics": [ "rba_uniprot_coordinates_location_genome" ] }, { "page": "rba_uniprot_coordinates_location_protein", "title": "Get Genome coordinate by Protein Sequence position", "concept": [ "\"UniProt - Coordinates\"" ], "topics": [ "rba_uniprot_coordinates_location_protein" ] }, { "page": "rba_uniprot_coordinates_search", "title": "Search Genomic Coordinates of UniProt entries", "concept": [ "\"UniProt - Coordinates\"" ], "topics": [ "rba_uniprot_coordinates_search" ] }, { "page": "rba_uniprot_epitope", "title": "Retrieve Epitopes by Accession", "concept": [ "\"UniProt - Epitopes\"" ], "topics": [ "rba_uniprot_epitope" ] }, { "page": "rba_uniprot_epitope_search", "title": "Search UniProt Epitopes", "concept": [ "\"UniProt - Epitopes\"" ], "topics": [ "rba_uniprot_epitope_search" ] }, { "page": "rba_uniprot_features", "title": "Get UniProt protein sequence features by accession", "concept": [ "\"UniProt - Features\"" ], "topics": [ "rba_uniprot_features" ] }, { "page": "rba_uniprot_features_search", "title": "Search UniProt protein sequence features", "concept": [ "\"UniProt - Features\"" ], "topics": [ "rba_uniprot_features_search" ] }, { "page": "rba_uniprot_genecentric", "title": "Get Gene-Centric proteins by UniProt Accession", "concept": [ "\"UniProt - Proteomes\"" ], "topics": [ "rba_uniprot_genecentric" ] }, { "page": "rba_uniprot_genecentric_search", "title": "Search Gene-Centric Proteins", "concept": [ "\"UniProt - Proteomes\"" ], "topics": [ "rba_uniprot_genecentric_search" ] }, { "page": "rba_uniprot_mutagenesis", "title": "Get Mutagenesis by UniProt Accession", "concept": [ "\"UniProt - Mutagenesis\"" ], "topics": [ "rba_uniprot_mutagenesis" ] }, { "page": "rba_uniprot_mutagenesis_search", "title": "Search Mutagenesis in UniProt", "concept": [ "\"UniProt - Mutagenesis\"" ], "topics": [ "rba_uniprot_mutagenesis_search" ] }, { "page": "rba_uniprot_proteins", "title": "Get UniProt entry by accession", "concept": [ "\"UniProt - Proteins\"" ], "topics": [ "rba_uniprot_proteins" ] }, { "page": "rba_uniprot_proteins_crossref", "title": "Get UniProt Entry by UniProt Cross-Reference Database and ID", "concept": [ "\"UniProt - Proteins\"" ], "topics": [ "rba_uniprot_proteins_crossref" ] }, { "page": "rba_uniprot_proteins_search", "title": "Search UniProt entries", "concept": [ "\"UniProt - Proteins\"" ], "topics": [ "rba_uniprot_proteins_search" ] }, { "page": "rba_uniprot_proteomes", "title": "Get proteome by proteome/proteins UPID", "concept": [ "\"UniProt - Proteomes\"" ], "topics": [ "rba_uniprot_proteomes" ] }, { "page": "rba_uniprot_proteomes_search", "title": "Search Proteomes in UniProt", "concept": [ "\"UniProt - Proteomes\"" ], "topics": [ "rba_uniprot_proteomes_search" ] }, { "page": "rba_uniprot_proteomics", "title": "Get Proteomics Peptides Mapped to UniProt Protein (Deprecated)", "concept": [ "\"Deprecated functions\"" ], "topics": [ "rba_uniprot_proteomics" ] }, { "page": "rba_uniprot_proteomics_hpp", "title": "Get HPP Proteomics data in UniProt", "concept": [ "\"UniProt - Proteomics\"" ], "topics": [ "rba_uniprot_proteomics_hpp" ] }, { "page": "rba_uniprot_proteomics_hpp_search", "title": "Search HPP Proteomics data in UniProt", "concept": [ "\"UniProt - Proteomics\"" ], "topics": [ "rba_uniprot_proteomics_hpp_search" ] }, { "page": "rba_uniprot_proteomics_non_ptm", "title": "Get Proteomics data in UniProt", "concept": [ "\"UniProt - Proteomics\"" ], "topics": [ "rba_uniprot_proteomics_non_ptm" ] }, { "page": "rba_uniprot_proteomics_non_ptm_search", "title": "Search Proteomics data in UniProt", "concept": [ "\"UniProt - Proteomics\"" ], "topics": [ "rba_uniprot_proteomics_non_ptm_search" ] }, { "page": "rba_uniprot_proteomics_ptm", "title": "Get Post-Translational Modification of UniProt Protein", "concept": [ "\"UniProt - Proteomics\"" ], "topics": [ "rba_uniprot_proteomics_ptm" ] }, { "page": "rba_uniprot_proteomics_ptm_search", "title": "Search Post-Translational Modification Proteomics in UniProt", "concept": [ "\"UniProt - Proteomics\"" ], "topics": [ "rba_uniprot_proteomics_ptm_search" ] }, { "page": "rba_uniprot_proteomics_search", "title": "Search Proteomics Peptides in UniProt (Deprecated)", "concept": [ "\"Deprecated functions\"" ], "topics": [ "rba_uniprot_proteomics_search" ] }, { "page": "rba_uniprot_proteomics_species", "title": "Get UniProt Proteomics Metadata", "concept": [ "\"UniProt - Proteomics\"" ], "topics": [ "rba_uniprot_proteomics_species" ] }, { "page": "rba_uniprot_ptm", "title": "Get Post-Translational Modification of UniProt Protein (Deprecated)", "concept": [ "\"Deprecated functions\"" ], "topics": [ "rba_uniprot_ptm" ] }, { "page": "rba_uniprot_ptm_search", "title": "Search Post-Translational Modification in UniProt (Deprecated)", "concept": [ "\"Deprecated functions\"" ], "topics": [ "rba_uniprot_ptm_search" ] }, { "page": "rba_uniprot_rna_edit", "title": "Retrieve Epitope by Accession", "concept": [ "\"UniProt - Epitopes\"" ], "topics": [ "rba_uniprot_rna_edit" ] }, { "page": "rba_uniprot_rna_edit_search", "title": "Search RNA Editing in UniProt", "concept": [ "\"UniProt - RNA Editing\"" ], "topics": [ "rba_uniprot_rna_edit_search" ] }, { "page": "rba_uniprot_taxonomy", "title": "Get UniProt Taxonomy Nodes", "concept": [ "\"UniProt - Taxonomy\"" ], "topics": [ "rba_uniprot_taxonomy" ] }, { "page": "rba_uniprot_taxonomy_lca", "title": "Get Lowest Common Ancestor (LCA) of Two Taxonomy Nodes", "concept": [ "\"UniProt - Taxonomy\"" ], "topics": [ "rba_uniprot_taxonomy_lca" ] }, { "page": "rba_uniprot_taxonomy_lineage", "title": "Get Taxonomic Lineage", "concept": [ "\"UniProt - Taxonomy\"" ], "topics": [ "rba_uniprot_taxonomy_lineage" ] }, { "page": "rba_uniprot_taxonomy_name", "title": "Search UniProt Taxonomic Names", "concept": [ "\"UniProt - Taxonomy\"" ], "topics": [ "rba_uniprot_taxonomy_name" ] }, { "page": "rba_uniprot_taxonomy_path", "title": "Traverse UniProt Taxonomic Tree Path", "concept": [ "\"UniProt - Taxonomy\"" ], "topics": [ "rba_uniprot_taxonomy_path" ] }, { "page": "rba_uniprot_taxonomy_relationship", "title": "Get Shortest Path Between Two Taxonomy Nodes", "concept": [ "\"UniProt - Taxonomy\"" ], "topics": [ "rba_uniprot_taxonomy_relationship" ] }, { "page": "rba_uniprot_uniparc", "title": "Get UniParc entry", "concept": [ "\"UniProt - UniParc\"" ], "topics": [ "rba_uniprot_uniparc" ] }, { "page": "rba_uniprot_uniparc_bestguess", "title": "Get UniParc Longest Sequence for Entries", "concept": [ "\"UniProt - UniParc\"" ], "topics": [ "rba_uniprot_uniparc_bestguess" ] }, { "page": "rba_uniprot_uniparc_search", "title": "Search UniParc Entries", "concept": [ "\"UniProt - UniParc\"" ], "topics": [ "rba_uniprot_uniparc_search" ] }, { "page": "rba_uniprot_uniparc_sequence", "title": "Get UniParc Entries by Sequence", "concept": [ "\"UniProt - UniParc\"" ], "topics": [ "rba_uniprot_uniparc_sequence" ] }, { "page": "rba_uniprot_variation", "title": "Get natural variants in UniProt by NIH-NCBI SNP database identifier", "concept": [ "\"UniProt - Variation\"" ], "topics": [ "rba_uniprot_variation" ] }, { "page": "rba_uniprot_variation_search", "title": "Search UniProt Natural Variants", "concept": [ "\"UniProt - Variation\"" ], "topics": [ "rba_uniprot_variation_search" ] } ], "_pkglogo": "https://github.com/moosa-r/rbioapi/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/moosa-r/rbioapi/raw/HEAD/README.md", "_rundeps": [ "askpass", "curl", "httr", "jsonlite", "mime", "openssl", "R6", "sys" ], "_vignettes": [ { "source": "rbioapi.Rmd", "filename": "rbioapi.html", "title": "1: rbioapi: User-Friendly R Interface to Biologic Web Services' API", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "What does rbioapi do?", "What is Supported by rbioapi?", "How to install?", "Naming conventions", "Changing the options", "Change the option globally", "Change the option only within a function call", "Connection test", "Iterating over paginated results", "How and what to cite?", "How to cite rbioapi", "How to cite the databases and web services", "Code of conduct", "What next?", "Design of rbioapi", "Links", "Session info" ], "created": "2021-04-28 11:44:27", "modified": "2025-01-26 21:03:33", "commits": 32 }, { "source": "rbioapi_enrichr.Rmd", "filename": "rbioapi_enrichr.html", "title": "2.A: Enrichr & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Gene set library concept in Enrichr", "Enrichment analysis using Enrichr", "Approach 1: Using the one-step Wrapper function", "Approach 2: Going step-by-step", "Working with Other Species", "Providing background gene list", "See also in Functions' manuals", "How to Cite?", "Over-representation analysis Using Other Services", "Links", "Session info" ], "created": "2021-04-25 00:26:22", "modified": "2025-06-29 17:51:27", "commits": 27 }, { "source": "rbioapi_jaspar.Rmd", "filename": "rbioapi_jaspar.html", "title": "2.B: JASPAR & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Data Organization in JASPAR", "Releases", "Collections", "Taxonomic Groups", "Species", "Matrix Profiles", "Search Matrix Profiles", "List Matrix Profiles Associated to a Base identifier", "Get a Matrix Profile", "Get Matrix and Annotations as an R Object", "Save a Matrix a File in Specific Format", "Get Binding Sites of a Matrix Profiles", "TF flexible models (TFFMs)", "How to Cite?", "Links", "Session info" ], "created": "2021-05-21 10:36:44", "modified": "2025-01-26 21:03:33", "commits": 16 }, { "source": "rbioapi_mieaa.Rmd", "filename": "rbioapi_mieaa.html", "title": "2.C: miEEA & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "First, find enrichment categories", "Submit Enrichment analysis request to miEAA", "Approach 1: Using the Wrapper function", "Approach 2: Going step-by-step", "Convert miRNA accessions", "How to Cite?", "Links", "Session info" ], "created": "2021-04-25 00:26:22", "modified": "2025-01-26 21:03:33", "commits": 22 }, { "source": "rbioapi_panther.Rmd", "filename": "rbioapi_panther.html", "title": "2.D: PANTHER & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Map genes", "Get information", "Gene List Analysis", "Get the available annotation datasets", "Submit the analysis request", "Over-representation analysis", "Statistical enrichment analysis", "Tree grafter", "How to Cite?", "Links", "Session info" ], "created": "2021-04-25 00:26:22", "modified": "2025-01-26 21:03:33", "commits": 23 }, { "source": "rbioapi_reactome.Rmd", "filename": "rbioapi_reactome.html", "title": "2.E: Reactome & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Reactome analysis services", "See also in Functions' manuals", "Reactome contents services", "Retrieve any object from Reactome knowledge-base", "Find Cross-Reference IDs in Reactome", "Map Cross-Reference IDs to Reactome", "See also in Functions' manuals", "Retrieve Reactome Database information", "General Mapping/Querying", "Things you can do with a Entities", "Things you can do with Events", "Pathways", "Interactors", "People", "Export diagrams and events", "How to Cite?", "Links", "Session info" ], "created": "2021-04-25 00:26:22", "modified": "2025-01-26 21:03:33", "commits": 20 }, { "source": "rbioapi_string.Rmd", "filename": "rbioapi_string.html", "title": "2.F: STRING & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Note about species argument", "Map your IDs to STRING IDs", "Get interaction network of a protein set", "Get interaction partners of a protein set", "Get network image of a protein set", "Enrichment analysis using STRING", "Functional enrichment", "Functional enrichment Plot", "Protein-protein interaction enrichment", "Get functional annotations", "See also in Functions' manuals", "How to Cite?", "Links", "Session info" ], "created": "2021-04-25 00:26:22", "modified": "2025-06-29 22:34:23", "commits": 23 }, { "source": "rbioapi_uniprot.Rmd", "filename": "rbioapi_uniprot.html", "title": "2.G: UniProt & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Search vs Retrieve", "Functions with *_search variant", "UniProt functions categories", "Proteins", "Proteins:", "Features", "Variation", "Antigens", "Epitopes", "Mutagenesis", "RNA-Editing", "Proteomics", "Proteomes", "Taxonomy", "Coordinates", "UniParc", "How to Cite?", "Links", "Session info" ], "created": "2021-04-25 00:26:22", "modified": "2025-01-26 21:03:33", "commits": 20 }, { "source": "rbioapi_do_enrich.Rmd", "filename": "rbioapi_do_enrich.html", "title": "3.A: Do with rbioapi: Enrichment (Over-Representation) Analysis in R", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "How to install?", "What is Over-representation analysis?", "Setting up the data", "Enrichr", "Reactome Analysis services", "PANTHER", "STRING", "miEAA", "How to cite?", "Links", "Session info" ], "created": "2022-01-19 17:39:16", "modified": "2025-02-03 00:18:03", "commits": 27 } ], "_score": 7.434824296268493, "_indexed": true, "_nocasepkg": "rbioapi", "_universes": [ "moosa-r" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8.3", "date": "2026-05-26T06:57:40.000Z", "distro": "noble", "commit": "35c26b5f4f320ade12ec67a2b6802e129aabfbd6", "fileid": "ce919115830acef564a0ea25cf254f0f0fafc3b1a9552ce20ef4339b69bf65c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/moosa-r/actions/runs/26436964112" }, { "r": "4.6.0", "os": "linux", "version": "0.8.3", "date": "2026-05-26T06:57:15.000Z", "distro": "noble", "commit": "35c26b5f4f320ade12ec67a2b6802e129aabfbd6", "fileid": "ea17dd6a5789d02b12eb5021680c0a96aace00beff8f85abcd900c48819a6f8f", "status": "success", "check": "OK", "buildurl": 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