Package: rbioapi 0.8.2

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

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

Authors:Moosa Rezwani [aut, cre]

rbioapi_0.8.2.tar.gz
rbioapi_0.8.2.zip(r-4.5)rbioapi_0.8.2.zip(r-4.4)rbioapi_0.8.2.zip(r-4.3)
rbioapi_0.8.2.tgz(r-4.5-any)rbioapi_0.8.2.tgz(r-4.4-any)rbioapi_0.8.2.tgz(r-4.3-any)
rbioapi_0.8.2.tar.gz(r-4.5-noble)rbioapi_0.8.2.tar.gz(r-4.4-noble)
rbioapi_0.8.2.tgz(r-4.4-emscripten)rbioapi_0.8.2.tgz(r-4.3-emscripten)
rbioapi.pdf |rbioapi.html✨
rbioapi/json (API)
NEWS

# Install 'rbioapi' in R:
install.packages('rbioapi', repos = c('https://moosa-r.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/moosa-r/rbioapi/issues

Pkgdown site:https://rbioapi.moosa-r.com

On CRAN:

api-clientbioinformaticsbiologyenrichmentenrichment-analysisenrichrjasparmieaaover-representation-analysispantherreactomestringuniprot

7.55 score 18 stars 55 scripts 383 downloads 125 exports 8 dependencies

Last updated 17 days agofrom:85fe3d5bfd. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 03 2025
R-4.5-winOKFeb 03 2025
R-4.5-macOKFeb 03 2025
R-4.5-linuxOKFeb 03 2025
R-4.4-winOKFeb 03 2025
R-4.4-macOKFeb 03 2025
R-4.3-winOKFeb 03 2025
R-4.3-macOKFeb 03 2025

Exports:rba_connection_testrba_enrichrrba_enrichr_add_backgroundrba_enrichr_add_listrba_enrichr_enrichrba_enrichr_gene_maprba_enrichr_libsrba_enrichr_view_listrba_jaspar_collectionsrba_jaspar_collections_matricesrba_jaspar_matrixrba_jaspar_matrix_searchrba_jaspar_matrix_versionsrba_jaspar_releasesrba_jaspar_sitesrba_jaspar_speciesrba_jaspar_species_matricesrba_jaspar_taxonsrba_jaspar_taxons_matricesrba_jaspar_tffmrba_jaspar_tffm_searchrba_mieaa_catsrba_mieaa_convert_typerba_mieaa_convert_versionrba_mieaa_enrichrba_mieaa_enrich_resultsrba_mieaa_enrich_statusrba_mieaa_enrich_submitrba_optionsrba_pagesrba_panther_enrichrba_panther_familyrba_panther_homologrba_panther_inforba_panther_mappingrba_panther_orthologrba_panther_tree_grafterrba_reactome_analysisrba_reactome_analysis_downloadrba_reactome_analysis_importrba_reactome_analysis_mappingrba_reactome_analysis_pdfrba_reactome_analysis_speciesrba_reactome_analysis_tokenrba_reactome_complex_listrba_reactome_complex_subunitsrba_reactome_diseasesrba_reactome_entity_other_formsrba_reactome_event_ancestorsrba_reactome_event_hierarchyrba_reactome_exporter_diagramrba_reactome_exporter_eventrba_reactome_exporter_overviewrba_reactome_exporter_reactionrba_reactome_interactors_psicquicrba_reactome_interactors_staticrba_reactome_mappingrba_reactome_orthologyrba_reactome_participant_ofrba_reactome_participantsrba_reactome_pathways_eventsrba_reactome_pathways_lowrba_reactome_pathways_toprba_reactome_people_idrba_reactome_people_namerba_reactome_queryrba_reactome_speciesrba_reactome_versionrba_reactome_xrefrba_string_annotationsrba_string_enrichmentrba_string_enrichment_imagerba_string_enrichment_ppirba_string_homology_interrba_string_homology_intrarba_string_interaction_partnersrba_string_interactions_networkrba_string_map_idsrba_string_network_imagerba_string_versionrba_uniprot_antigensrba_uniprot_antigens_searchrba_uniprot_coordinatesrba_uniprot_coordinates_locationrba_uniprot_coordinates_location_genomerba_uniprot_coordinates_location_proteinrba_uniprot_coordinates_searchrba_uniprot_epitoperba_uniprot_epitope_searchrba_uniprot_featuresrba_uniprot_features_searchrba_uniprot_genecentricrba_uniprot_genecentric_searchrba_uniprot_mutagenesisrba_uniprot_mutagenesis_searchrba_uniprot_proteinsrba_uniprot_proteins_crossrefrba_uniprot_proteins_searchrba_uniprot_proteomesrba_uniprot_proteomes_searchrba_uniprot_proteomicsrba_uniprot_proteomics_hpprba_uniprot_proteomics_hpp_searchrba_uniprot_proteomics_non_ptmrba_uniprot_proteomics_non_ptm_searchrba_uniprot_proteomics_ptmrba_uniprot_proteomics_ptm_searchrba_uniprot_proteomics_searchrba_uniprot_proteomics_speciesrba_uniprot_ptmrba_uniprot_ptm_searchrba_uniprot_rna_editrba_uniprot_rna_edit_searchrba_uniprot_taxonomyrba_uniprot_taxonomy_lcarba_uniprot_taxonomy_lineagerba_uniprot_taxonomy_namerba_uniprot_taxonomy_pathrba_uniprot_taxonomy_relationshiprba_uniprot_uniparcrba_uniprot_uniparc_bestguessrba_uniprot_uniparc_searchrba_uniprot_uniparc_sequencerba_uniprot_variationrba_uniprot_variation_search

Dependencies:askpasscurlhttrjsonlitemimeopensslR6sys

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

Moosa Rezwani

Rendered fromrbioapi.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-01-26
Started: 2021-04-28

2.A: Enrichr & rbioapi

Moosa Rezwani

Rendered fromrbioapi_enrichr.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-02-03
Started: 2021-04-25

2.B: JASPAR & rbioapi

Moosa Rezwani

Rendered fromrbioapi_jaspar.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-01-26
Started: 2021-05-21

2.C: miEEA & rbioapi

Moosa Rezwani

Rendered fromrbioapi_mieaa.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-01-26
Started: 2021-04-25

2.D: PANTHER & rbioapi

Moosa Rezwani

Rendered fromrbioapi_panther.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-01-26
Started: 2021-04-25

2.E: Reactome & rbioapi

Moosa Rezwani

Rendered fromrbioapi_reactome.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-01-26
Started: 2021-04-25

2.F: STRING & rbioapi

Moosa Rezwani

Rendered fromrbioapi_string.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-01-26
Started: 2021-04-25

2.G: UniProt & rbioapi

Moosa Rezwani

Rendered fromrbioapi_uniprot.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-01-26
Started: 2021-04-25

3.A: Do with rbioapi: Enrichment (Over-Representation) Analysis in R

Moosa Rezwani

Rendered fromrbioapi_do_enrich.Rmdusingknitr::rmarkdownon Feb 03 2025.

Last update: 2025-02-03
Started: 2022-01-19

Readme and manuals

Help Manual

Help pageTopics
Test if the Supported Services Are Respondingrba_connection_test
A One-step Wrapper for Gene-list Enrichment Using Enrichrrba_enrichr
Upload Background Gene-List to Enrichrrba_enrichr_add_background
Upload Your Gene-List to Enrichrrba_enrichr_add_list
Get Enrichr Enrichment Resultsrba_enrichr_enrich
Find Enrichr Terms That Contain a Given Generba_enrichr_gene_map
Retrieve a List of available libraries from Enrichrrba_enrichr_libs
View an Uploaded Gene Listrba_enrichr_view_list
List collections available in JASPARrba_jaspar_collections
List matrices available in a JASPAR collectionrba_jaspar_collections_matrices
Get a Position Frequency Matrices (PFM) with annotationsrba_jaspar_matrix
Search matrix profiles available in JASPARrba_jaspar_matrix_search
List matrix profile versions associated with a base IDrba_jaspar_matrix_versions
Get information about JASPAR database releasesrba_jaspar_releases
Get binding sites of a matrix profilerba_jaspar_sites
List available species in JASPARrba_jaspar_species
List matrices available in JASPAR of a speciesrba_jaspar_species_matrices
List available taxonomic groups in JASPARrba_jaspar_taxons
List matrices available in JASPAR of a taxonomic grouprba_jaspar_taxons_matrices
Get a TF flexible models (TFFMs) informationrba_jaspar_tffm
Search TF flexible models (TFFMs) available in JASPARrba_jaspar_tffm_search
Get Supported Enrichment Categories for a Species and miRNA Typerba_mieaa_cats
Convert Between Mature and precursor miRNA Accessionrba_mieaa_convert_type
Convert miRNA accession Between Different miRBase Versionsrba_mieaa_convert_version
A One-step Wrapper for miRNA Enrichment Using miEAArba_mieaa_enrich
Retrieve Results of a finished Enrichment Analysis from miEAArba_mieaa_enrich_results
Check Status of a Submitted Enrichment Analysis in miEAArba_mieaa_enrich_status
Submit miEAA miRNA Enrichment Analysis Requestrba_mieaa_enrich_submit
Set rbioapi Global Optionsrba_options
Get Multiple Pages of a Paginated Resourcerba_pages
PANTHER Over-Representation or Enrichment Analysisrba_panther_enrich
Get PANTHER Families and Sub-Familiesrba_panther_family
Search PANTHER for Homologs of Gene(s)rba_panther_homolog
Get PANTHER database Informationrba_panther_info
Map A Gene-set to PANTHER Databaserba_panther_mapping
Search PANTHER for Orthologs of Gene(s)rba_panther_ortholog
PANTHER Tree Grafterrba_panther_tree_grafter
Reactome Over-Representation or Expression Analysisrba_reactome_analysis
Download Different Reactome Analysis Resultsrba_reactome_analysis_download
Import Saved Analysis JSON to Reactomerba_reactome_analysis_import
Maps Molecule Identifiersrba_reactome_analysis_mapping
Generate PDF file with Reactome Analysis Resultsrba_reactome_analysis_pdf
Compare Human Pathways with with Other Speciesrba_reactome_analysis_species
Return the Results Associated with a Tokenrba_reactome_analysis_token
Get Complexes That Include a Moleculerba_reactome_complex_list
Get a Complex's Subunitsrba_reactome_complex_subunits
Reactome Diseasesrba_reactome_diseases
Get Other forms of a Reactome Entityrba_reactome_entity_other_forms
Get Reactome Events Ancestorsrba_reactome_event_ancestors
Get Full Event Hierarchy of a Speciesrba_reactome_event_hierarchy
Get a Reactome Event Diagramrba_reactome_exporter_diagram
Exports A Reactome Event to SBGN or SBMLrba_reactome_exporter_event
Get a Reactome Pathway Overviewrba_reactome_exporter_overview
Get a Reactome Reaction Eventrba_reactome_exporter_reaction
The interface From Reactome to PSICQUICrba_reactome_interactors_psicquic
Get Static(IntAct) Interaction Information of a Proteinrba_reactome_interactors_static
Map External ID to Reactome Pathways/Reactionsrba_reactome_mapping
Get Orthologous (Computationally Inferred) Eventsrba_reactome_orthology
Get Larger Reactome Structures Which Include an Entityrba_reactome_participant_of
Get Participants of a Reactome Eventrba_reactome_participants
Get Events Contained in an Upstream Eventsrba_reactome_pathways_events
Get lower level pathways Containing a 'Physical Entity' or Eventrba_reactome_pathways_low
Get Top Level Pathways in a Speciesrba_reactome_pathways_top
A person by his identifiersrba_reactome_people_id
Get Persons Information by Namerba_reactome_people_name
Query and Retrieve any Reactome knowledge-base Objectrba_reactome_query
Get Reactome Speciesrba_reactome_species
The version number of current databaserba_reactome_version
Map Cross References IDs to Reactome ReferenceEntityrba_reactome_xref
Retrieving Functional Annotationrba_string_annotations
Getting Functional Enrichmentrba_string_enrichment
Get STRING Enrichment Plotrba_string_enrichment_image
Get Protein-Protein Interaction Enrichmentrba_string_enrichment_ppi
Get Similarity Scores Hits of Proteins in Different Speciesrba_string_homology_inter
Get Similarity Scores Hits of Proteins in a Speciesrba_string_homology_intra
Get All STRING Interaction Partnersrba_string_interaction_partners
Get STRING Network Interactionsrba_string_interactions_network
Map a Set of Identifiers to STRING Identifiersrba_string_map_ids
Get STRING Network Imagerba_string_network_image
Get Current STRING Versionrba_string_version
Get Antigens by UniProt Accessionrba_uniprot_antigens
Search Antigens in UniProtrba_uniprot_antigens_search
Get Genomic Coordinates of a Proteinrba_uniprot_coordinates
Search UniProt entries by taxonomy and genomic coordinatesrba_uniprot_coordinates_location
Get Genome coordinate by Gene Sequence positionrba_uniprot_coordinates_location_genome
Get Genome coordinate by Protein Sequence positionrba_uniprot_coordinates_location_protein
Search Genomic Coordinates of UniProt entriesrba_uniprot_coordinates_search
Retrieve Epitopes by Accessionrba_uniprot_epitope
Search UniProt Epitopesrba_uniprot_epitope_search
Get UniProt protein sequence features by accessionrba_uniprot_features
Search UniProt protein sequence featuresrba_uniprot_features_search
Get Gene-Centric proteins by UniProt Accessionrba_uniprot_genecentric
Search Gene-Centric Proteinsrba_uniprot_genecentric_search
Get Mutagenesis by UniProt Accessionrba_uniprot_mutagenesis
Search Mutagenesis in UniProtrba_uniprot_mutagenesis_search
Get UniProt entry by accessionrba_uniprot_proteins
Get UniProt Entry by UniProt Cross-Reference Database and IDrba_uniprot_proteins_crossref
Search UniProt entriesrba_uniprot_proteins_search
Get proteome by proteome/proteins UPIDrba_uniprot_proteomes
Search Proteomes in UniProtrba_uniprot_proteomes_search
Get Proteomics Peptides Mapped to UniProt Protein (Deprecated)rba_uniprot_proteomics
Get HPP Proteomics data in UniProtrba_uniprot_proteomics_hpp
Search HPP Proteomics data in UniProtrba_uniprot_proteomics_hpp_search
Get Proteomics data in UniProtrba_uniprot_proteomics_non_ptm
Search Proteomics data in UniProtrba_uniprot_proteomics_non_ptm_search
Get Post-Translational Modification of UniProt Proteinrba_uniprot_proteomics_ptm
Search Post-Translational Modification Proteomics in UniProtrba_uniprot_proteomics_ptm_search
Search Proteomics Peptides in UniProt (Deprecated)rba_uniprot_proteomics_search
Get UniProt Proteomics Metadatarba_uniprot_proteomics_species
Get Post-Translational Modification of UniProt Protein (Deprecated)rba_uniprot_ptm
Search Post-Translational Modification in UniProt (Deprecated)rba_uniprot_ptm_search
Retrieve Epitope by Accessionrba_uniprot_rna_edit
Search RNA Editing in UniProtrba_uniprot_rna_edit_search
Get UniProt Taxonomy Nodesrba_uniprot_taxonomy
Get Lowest Common Ancestor (LCA) of Two Taxonomy Nodesrba_uniprot_taxonomy_lca
Get Taxonomic Lineagerba_uniprot_taxonomy_lineage
Search UniProt Taxonomic Namesrba_uniprot_taxonomy_name
Traverse UniProt Taxonomic Tree Pathrba_uniprot_taxonomy_path
Get Shortest Path Between Two Taxonomy Nodesrba_uniprot_taxonomy_relationship
Get UniParc entryrba_uniprot_uniparc
Get UniParc Longest Sequence for Entriesrba_uniprot_uniparc_bestguess
Search UniParc Entriesrba_uniprot_uniparc_search
Get UniParc Entries by Sequencerba_uniprot_uniparc_sequence
Get natural variants in UniProt by NIH-NCBI SNP database identifierrba_uniprot_variation
Search UniProt Natural Variantsrba_uniprot_variation_search