Package: rbioapi 0.8.0

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_0.8.0.tar.gz
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rbioapi_0.8.0.tgz(r-4.4-any)rbioapi_0.8.0.tgz(r-4.3-any)
rbioapi_0.8.0.tar.gz(r-4.5-noble)rbioapi_0.8.0.tar.gz(r-4.4-noble)
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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'))

Peer review:

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

On CRAN:

api-clientbioinformaticsbiologyenrichmentenrichment-analysisenrichrjasparmieaaover-representation-analysispantherreactomestringuniprot

6.89 score 17 stars 51 scripts 372 downloads 111 exports 8 dependencies

Last updated 8 months agofrom:8f6c955204. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winOKNov 14 2024
R-4.5-linuxOKNov 14 2024
R-4.4-winOKNov 14 2024
R-4.4-macOKNov 14 2024
R-4.3-winOKNov 14 2024
R-4.3-macOKNov 14 2024

Exports:rba_connection_testrba_enrichrrba_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_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_searchrba_uniprot_coordinates_sequencerba_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_searchrba_uniprot_ptmrba_uniprot_ptm_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 Nov 14 2024.

Last update: 2023-12-01
Started: 2021-04-28

2.A: Enrichr & rbioapi

Moosa Rezwani

Rendered fromrbioapi_enrichr.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-05-09
Started: 2021-04-25

2.B: JASPAR & rbioapi

Moosa Rezwani

Rendered fromrbioapi_jaspar.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-12-01
Started: 2021-05-21

2.C: miEEA & rbioapi

Moosa Rezwani

Rendered fromrbioapi_mieaa.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-07-27
Started: 2021-04-25

2.D: PANTHER & rbioapi

Moosa Rezwani

Rendered fromrbioapi_panther.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-09-15
Started: 2021-04-25

2.E: Reactome & rbioapi

Moosa Rezwani

Rendered fromrbioapi_reactome.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-05-09
Started: 2021-04-25

2.F: STRING & rbioapi

Moosa Rezwani

Rendered fromrbioapi_string.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-09-09
Started: 2021-04-25

2.G: UniProt & rbioapi

Moosa Rezwani

Rendered fromrbioapi_uniprot.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-05-09
Started: 2021-04-25

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

Moosa Rezwani

Rendered fromrbioapi_do_enrich.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-09-15
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 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 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 Grafter Use this function to retrieve a PANTHER family's tree topology information with a node corresponding to your sequence grafted in the best location in that tree.rba_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 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
Search Genomic Coordinates of UniProt entriesrba_uniprot_coordinates_search
Get Genome coordinate by Protein Sequence positionrba_uniprot_coordinates_sequence
Get UniProt protein sequence features by accessionrba_uniprot_features
UniProt maintains sequence annotations (features) that describe regions in the protein sequence. Using this function, you can search and retrieve UniProt proteins' sequence annotations (features). you may also refine your search query with variety of modifiers.rba_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 Proteinrba_uniprot_proteomics
Search Proteomics Peptides in UniProtrba_uniprot_proteomics_search
Get Post-Translational Modification of UniProt Proteinrba_uniprot_ptm
Search Post-Translational Modification in UniProtrba_uniprot_ptm_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