{ "_id": "6ad3fd3e8b78ae42bccc4b5c", "Type": "Package", "Package": "rbioapi", "Title": "User-Friendly R Interface to Biologic Web Services' API", "Version": "0.8.3.9000", "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", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libpng-dev libssl-dev", "Repository": "https://moosa-r.r-universe.dev", "Date/Publication": "2026-10-17 20:56:53 UTC", "RemoteUrl": "https://github.com/moosa-r/rbioapi", "RemoteRef": "HEAD", "RemoteSha": "9764b88ed8ce2eb465c32c4414432884b9488bd8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-17 22:52:30 UTC", "User": "root" }, "Author": "Moosa Rezwani [aut, cre] (ORCID:\n)", "Maintainer": "Moosa Rezwani ", "_user": "moosa-r", "_type": "src", "_file": "rbioapi_0.8.3.9000.tar.gz", "_fileid": "https://r2.ropensci.org/05aec188b95be09028c25f1301275fb2f898a8eaee21f5a87902dbbc9ccf201e", "_filesize": 2226817, "_sha256": "05aec188b95be09028c25f1301275fb2f898a8eaee21f5a87902dbbc9ccf201e", "_expires": "2027-01-25T22:57:00.000Z", "_created": "2026-10-17T22:52:30.000Z", "_published": "2026-10-17T22:57:02.475Z", "_buildurl": "https://github.com/r-universe/moosa-r/actions/runs/39076417923", "_status": "failure", "_host": "GitHub-Actions", "_jobs": [ { "job": 117525775332, "time": 125, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12117407092" }, { "job": 117525774874, "time": 131, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12117043871" }, { "job": 117525774870, "time": 147, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12117755350" }, { "job": 117525774904, "time": 178, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12117093636" }, { "job": 117524437366, "time": 414, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "12116578986" }, { "job": 117525774864, "time": 117, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12117870393" }, { "job": 117525774934, "time": 124, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12117700982" }, { "job": 117525774906, "time": 89, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12117636188" }, { "job": 117525774872, "time": 60, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12117636142" } ], "_upstream": "https://github.com/moosa-r/rbioapi", "_commit": { "id": "9764b88ed8ce2eb465c32c4414432884b9488bd8", "author": "Moosa Rezwani ", "committer": "Moosa Rezwani ", "message": "Move STRING implementation to version 12.5\n\nMove STRING requests to the stable 12.5 server and extend network and enrichment support to match the current API, while correcting request construction, validation, response handling, and documentation.\n\n- support directed regulatory networks and typed functional networks in network, interaction-partner, and image functions\n- expose physical and regulatory overlays and regulatory-sign controls, and normalize missing typed evidence scores to numeric NA\n- add optional enrichment strength and signal columns, filtering, and term merging by input-gene overlap\n- extend enrichment figures with independent sorting, bar plots, GWAS and Hallmark categories, and the red_blue palette\n- normalize axis and sorting values while retaining existing aliases and explicitly forwarding the signal axis default\n- correct multiple-target-species homology requests and floating-point validation of enrichment-figure grouping thresholds\n- handle optional logical and font-size arguments consistently during request construction\n- validate new filters and network-mode combinations, enforce the 100-term figure limit, and reject NULL image formats early\n- return zero-length numeric image arrays instead of NULL for empty PNG enrichment responses, including high-resolution images\n- refresh STRING parameter and return documentation, update the 2025 citation and README version output, and regenerate the manuals\n- expand and organize vignette examples and displayed figures, align figure captions and guards, and document the migration in NEWS\n", "time": 1792270613 }, "_maintainer": { "name": "Moosa Rezwani", "email": "moosa.rezwani@gmail.com", "login": "moosa-r", "orcid": "0000-0001-6325-4444", "description": "Immunologist for most of the time. 😃 ", "uuid": 62205735 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "httr", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "png", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "DT", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.1.7", "role": "Suggests" } ], "_owner": "moosa-r", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-05", "n": 1 }, { "week": "2026-30", "n": 23 }, { "week": "2026-31", "n": 6 }, { "week": "2026-32", "n": 4 }, { "week": "2026-33", "n": 16 }, { "week": "2026-34", "n": 4 }, { "week": "2026-35", "n": 4 }, { "week": "2026-36", "n": 1 }, { "week": "2026-39", "n": 1 }, { "week": "2026-42", "n": 1 } ], "_tags": [], "_topics": [ "api-client", "bioinformatics", "biology", "enrichment", "enrichment-analysis", "enrichr", "jaspar", "mieaa", "over-representation-analysis", "panther", "reactome", "string", "uniprot" ], "_stars": 24, "_contributors": [ { "user": "moosa-r", "count": 471, "uuid": 62205735 } ], "_userbio": { "uuid": 62205735, "type": "user", "name": "Moosa Rezwani", "followers": 11, "description": "Immunologist for most of the time. 😃 " }, "_downloads": { "count": 526, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rbioapi" }, "_devurl": "https://github.com/moosa-r/rbioapi", "_pkgdown": "https://rbioapi.moosa-r.com", "_searchresults": 95, "_rbuild": "4.6.1", "_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" ], "_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_gene_sets", "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_metadata", "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_genome", "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_search", "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_functional_terms", "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_features_type", "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_locations", "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_gene_sets", "title": "Retrieve Gene Sets From an Enrichr Library", "concept": [ "\"Enrichr\"" ], "topics": [ "rba_enrichr_gene_sets" ] }, { "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 matrix (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 information about a TF flexible model (TFFM)", "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_metadata", "title": "Retrieve API Request Metadata", "concept": [ "\"Helper functions\"" ], "topics": [ "rba_metadata" ] }, { "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 Identifiers", "concept": [ "\"miEAA\"" ], "topics": [ "rba_mieaa_convert_type" ] }, { "page": "rba_mieaa_convert_version", "title": "Convert miRNA Identifiers 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 the Results of a Finished miEAA Enrichment Analysis", "concept": [ "\"miEAA\"" ], "topics": [ "rba_mieaa_enrich_results" ] }, { "page": "rba_mieaa_enrich_status", "title": "Check the Status of a Submitted miEAA Enrichment Analysis", "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": "Retrieve 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_genome", "title": "Retrieve Genes from a PANTHER Genome", "concept": [ "\"PANTHER\"" ], "topics": [ "rba_panther_genome" ] }, { "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": "Retrieve the Reactome 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 Event", "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": "Get a Person by Identifier", "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": "Retrieve Reactome Knowledgebase Objects", "concept": [ "\"Reactome Content Service - Common Data Retrieval\"" ], "topics": [ "rba_reactome_query" ] }, { "page": "rba_reactome_search", "title": "Search the Reactome Knowledgebase", "concept": [ "\"Reactome Content Service - Search\"" ], "topics": [ "rba_reactome_search" ] }, { "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-Reference Identifiers to Reactome", "concept": [ "\"Reactome Content Service - ReferenceEntity Queries\"" ], "topics": [ "rba_reactome_xref" ] }, { "page": "rba_string_annotations", "title": "Get Functional Annotations", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_annotations" ] }, { "page": "rba_string_enrichment", "title": "Get 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_functional_terms", "title": "Search STRING Functional Terms", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_functional_terms" ] }, { "page": "rba_string_homology_inter", "title": "Get Best Protein Similarity Hits Across Species", "concept": [ "\"STRING\"" ], "topics": [ "rba_string_homology_inter" ] }, { "page": "rba_string_homology_intra", "title": "Get Protein Similarity Scores Within 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": "Map Genomic Coordinates to Protein Sequence Positions", "concept": [ "\"UniProt - Coordinates\"" ], "topics": [ "rba_uniprot_coordinates_location_genome" ] }, { "page": "rba_uniprot_coordinates_location_protein", "title": "Map Protein Sequence Positions to Genomic Coordinates", "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_features_type", "title": "Search UniProt protein sequence features by description", "concept": [ "\"UniProt - Features\"" ], "topics": [ "rba_uniprot_features_type" ] }, { "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 a Proteome by 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 UniProt RNA-Editing Annotations by Accession", "concept": [ "\"UniProt - RNA Editing\"" ], "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": "Retrieve UniProt Natural Variants by Identifier", "concept": [ "\"UniProt - Variation\"" ], "topics": [ "rba_uniprot_variation" ] }, { "page": "rba_uniprot_variation_locations", "title": "Retrieve UniProt Natural Variants by Sequence Position", "concept": [ "\"UniProt - Variation\"" ], "topics": [ "rba_uniprot_variation_locations" ] }, { "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", "png", "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", "Saving API request metadata", "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": "2026-08-29 01:16:59", "commits": 35 }, { "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", "Retrieve gene sets from an Enrichr library", "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": "2026-07-20 20:24:46", "commits": 29 }, { "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 as a File in a Specific Format", "Get Binding Sites for a Matrix Profile", "TF flexible models (TFFMs)", "How to Cite?", "Links", "Session info" ], "created": "2021-05-21 10:36:44", "modified": "2026-07-21 00:40:07", "commits": 18 }, { "source": "rbioapi_mieaa.Rmd", "filename": "rbioapi_mieaa.html", "title": "2.C: miEAA & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "First, find enrichment categories", "Submit an enrichment-analysis request to miEAA", "Approach 1: Using the wrapper function", "Approach 2: Going step-by-step", "Convert miRNA identifiers", "How to Cite?", "Links", "Session info" ], "created": "2021-04-25 00:26:22", "modified": "2026-07-28 02:33:43", "commits": 23 }, { "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": "2026-07-23 01:18:29", "commits": 25 }, { "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", "Search the Reactome knowledge-base", "Retrieve any object from Reactome knowledge-base", "Find Cross-Reference IDs in Reactome", "Map Cross-Reference IDs to Reactome", "See also in function manuals", "Retrieve Reactome database information", "General Mapping/Querying", "Things you can do with 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": "2026-08-23 13:58:08", "commits": 24 }, { "source": "rbioapi_string.Rmd", "filename": "rbioapi_string.html", "title": "2.F: STRING & rbioapi", "author": "Moosa Rezwani", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The 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": "2026-10-17 20:56:53", "commits": 27 }, { "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": "2026-08-11 22:34:19", "commits": 23 }, { "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": "2026-10-17 20:56:53", "commits": 33 } ], "_score": 8.011147360775798, "_indexed": true, "_nocasepkg": "rbioapi", "_universes": [ "moosa-r" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8.3.9000", "date": "2026-10-17T22:55:18.000Z", "distro": "resolute", "commit": "9764b88ed8ce2eb465c32c4414432884b9488bd8", "fileid": "https://r2.ropensci.org/7e0395b6bf71c90722fa95711ecdae88e02af4246f3fb495a2bd420f3b8a7039", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/moosa-r/actions/runs/39076417923" }, { "r": "4.6.1", "os": 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