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Changelog

Source: NEWS.md

rbioapi (development version)

New features

  • rba_metadata() retrieves optional request metadata attached to rbioapi results. Metadata can be enabled for one call with metadata = TRUE or for all later calls with rba_options(metadata = TRUE). It records the rbioapi version and, for each request, its time, call, original httr response, and the exact function(s) used to parse that response. Multi-request functions, or multiple calls due to retries preserve request order. Metadata remains off by default because it can substantially increase the size of returned R objects.

  • rba_pages() now supports inclusive "pages:start:end" ranges in either direction and arbitrary ordered page sets through page_arg and pages. It accepts at most 100 unique positive whole-number pages and waits at least two seconds between requests. Results preserve the requested order, retain NULL pages, and use names such as page_1. The skip_error, progress, and verbose arguments now provide explicit control over the complete operation.

  • rba_reactome_search() searches Reactome by text with filters for species, entry type, compartment, keyword, and scope, together with grouping and page controls.

  • rba_enrichr_gene_sets() retrieves all gene sets, or one exact term, from an organism-specific Enrichr library and can save the original GMT file.

  • rba_panther_genome() retrieves one page of genes from a PANTHER genome and reports the current page, total pages, and number of genes in the genome.

  • rba_string_functional_terms() searches STRING functional terms by ID or descriptive text for a species.

  • rba_uniprot_features_type() searches UniProt feature descriptions for a chosen feature type, with optional annotation filters.

  • rba_uniprot_variation_locations() retrieves UniProt variants for paired accession and sequence-position values. Results are returned as a list named by accession or saved as PEFF.

  • rba_panther_enrich() gains request_mapped_genes and can return genes mapped from the input, genes mapped from the reference set, or no mapped genes. Input-gene mappings are returned by default.

  • rba_string_interactions_network() and rba_string_network_image() can request a network with network_term_id instead of a list of IDs. rba_string_annotations() gains only_pubmed; when TRUE, it takes priority over allow_pubmed.

  • rba_reactome_event_hierarchy() gains pathway-only output and filters based on an analysis token. rba_reactome_query() gains controls for relationships, reference-entity summaries, and diseases. rba_reactome_xref() now accepts several IDs and supports database filters and result pages.

  • rba_mieaa_cats() gains a mode argument for all, default, or expert categories. rba_mieaa_enrich() gains poll_interval and poll_timeout to control how often a job is checked and how long polling continues.

Changes to existing behavior

  • rbioapi now rejects NA and NaN unless a function explicitly permits them. Numeric identifiers, counts, sequence positions, page numbers, and retry counts must be finite whole numbers where applicable. Invalid values passed to rba_options() now produce an error instead of silently restoring package defaults.

  • rba_mieaa_enrich_submit() no longer assumes human input and now requires species as a supported abbreviation, scientific name, or taxonomy ID.

  • rba_panther_info(what = "families") now names its family result family, correcting the previous familiy spelling.

  • rba_reactome_pathways_events() now returns complete contained-event records as a named list rather than a data frame. Requests for one event attribute preserve empty and structured values; if the response cannot be separated reliably by event, the original response is returned with a warning.

  • rba_string_map_ids() now uses STRING v12’s get_string_ids service and returns at most one match for each input ID. echo_query now defaults to TRUE, queryIndex is returned as an integer, and saved responses use .tsv. The limit argument is deprecated and has no effect.

  • rba_string_network_image() and rba_string_enrichment_image() now return PNG results as decoded image arrays and SVG results as raw content.

  • rba_uniprot_rna_edit_search() renames variantlocation to variant_location to match UniProt.

Other updates by service

  • Enrichr functions now use the correct export and Speedrichr view web addresses, accept positive whole-number list IDs, and use .tsv files for standard enrichment and .json files for background enrichment. Custom-background results preserve one row per enriched term instead of creating extra rows from the returned gene list (#20).

  • JASPAR functions now default to and accept the 2026 release. Requests for collections, matrices, releases, sites, species, taxon groups, and TFFMs use current query values and supported taxon groups. The TFFM search alias, saved file names, and JASPAR error details are also corrected.

  • miEAA functions now use the current /mieaa/ web addresses and check category names before submitting a job. Conversion results use .txt or .tsv files to match their content. Over-representation analysis (ORA), gene set enrichment analysis (GSEA), empty results, and numeric sorting are handled correctly. Failed, malformed, or timed-out jobs stop promptly while still respecting skip_error.

  • STRING requests now follow the current routes for ID mapping, interactions, homology, enrichment, annotations, and images. Set-based operations remove duplicate IDs and backgrounds, while ID mapping preserves duplicates and input order. Functions subject to STRING’s species limit now require species for more than 10 unique IDs. Empty enrichment results and image file names are also handled correctly.

  • PANTHER requests now follow the current service limits. Mapping accepts up to 5,000 IDs, enrichment checks the 100,000-ID limit, and TreeGrafter accepts sequences up to 50,000 characters. Paralog requests, family page counts, out-of-range pages, mapped-gene results, and temporary-file cleanup are corrected. Empty, single-record, and multi-record table-like results now have consistent data-frame forms while preserving nested fields.

  • Reactome analysis functions now use the current submission, mapping, report, and download routes. Scalar IDs, vectors, tables, local files, and HTTP(S) URLs are handled consistently, and local files use Reactome’s current form upload. Direct, token, and species analysis results now represent pathways as a data frame, including a zero-row data frame when no pathways are found.

  • Reactome content functions now use the current hierarchy, enhanced-query, interaction, orthology, cross-reference, and exporter resources. rba_reactome_analysis_token() makes species optional and defaults p_value to 1. rba_reactome_exporter_diagram() now defaults ehld to TRUE, matching Reactome’s current behavior.

  • UniProt protein, feature, variation, proteomics, proteome, gene-centric, coordinate, taxonomy, and UniParc functions now use current web addresses, argument names, filters, page handling, and returned data. Search results are named by accession more reliably, and deprecated proteomics functions call their supported replacements.

Other fixes and improvements

  • rbioapi now detects errors reported in a response body with HTTP 200 and applies skip_error in the same way as for regular HTTP errors.

  • Error messages from Enrichr, JASPAR, miEAA, PANTHER, Reactome, STRING, and UniProt now include the HTTP status and useful server details. Unrecognized response formats return the original text instead of hiding it. UniProt server errors are handled, and 4xx and 5xx responses are correctly described as client and server errors.

  • Response saving now more robustly supports Windows and Unix-like file paths containing backslashes, spaces, or quotes. Missing targets are handled consistently, and invalid paths produce clearer errors.

  • Required-argument detection, optional NULL handling, retry validation, and request-header construction now behave consistently and report invalid inputs more clearly.

Documentation and maintenance

  • Function manuals, argument and return descriptions, examples, vignettes, external links, and service citations are updated and standardized. Slow examples use smaller requests so checks and documentation builds take less time.

  • png moves from Suggests to Imports because STRING image functions use it while the package is running. The minimum suggested testthat version is now 3.1.7. Tests cover the new input checks, service errors, metadata, multiple pages, and file saving, and the GitHub Actions files use current templates.

  • Documentation is regenerated with roxygen2 8.0.0. The pkgdown reference lists the new functions, and README badges, links, examples, and development notices are updated.

rbioapi 0.8.3 (Current CRAN version)

CRAN release: 2025-07-03

  • Improved internal stability of Enrichr functions

  • Minor improvements and fixes.

rbioapi 0.8.2

CRAN release: 2025-02-07

  • Update functions to the latest corresponding API endpoints:

    • Added STRING function:

      rba_string_enrichment_image()

    • Updated Enrichr function:

      Added option to supply background genes

    • Updated PANTHER function:

      added option to supply data frame to the enrichment/over-representation function.

    • Added UniProt functions:

      rba_uniprot_epitope(), rba_uniprot_epitope_search(), rba_uniprot_coordinates_location_genome(), 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_species(), rba_uniprot_rna_edit(), rba_uniprot_rna_edit_search()

    • Deprecated UniProt functions:

      rba_uniprot_proteomics(), rba_uniprot_proteomics_search(), rba_uniprot_ptm(), rba_uniprot_ptm_search()

    • New arguments added to existing UniProt functions:

      rba_uniprot_features_search(), rba_uniprot_coordinates_location_protein(), rba_uniprot_features()

  • All scripts were reformatted to enhance readability.

  • Minor improvements and fixes.

rbioapi 0.8.1

CRAN release: 2024-03-30

  • Move to JASPAR 2024.

  • Minor improvements and fixes.

rbioapi 0.8.0

CRAN release: 2023-09-30

  • Move to STRING v12.

  • Incorporate the recent changes in PANTHER and miEAA API.

  • Minor improvements and fixes.

rbioapi 0.7.9

CRAN release: 2023-05-09

  • Stability improvements.

rbioapi 0.7.8

CRAN release: 2023-05-02

  • Bug fixes and minor improvements.

rbioapi 0.7.7

CRAN release: 2022-08-08

  • Bug fixes and minor improvements.

rbioapi 0.7.6

CRAN release: 2022-04-05

  • Submitted the paper to Bioinformatics journal (DOI: 10.1093/bioinformatics/btac172).

  • Added vignette article: “Over-Representation (Enrichment) Analysis””

  • Updated citations information.

  • Moved to JASPAR 2022.

  • Added new API endpoints of UniProt and PANTHER.

  • Minor internal improvements.

rbioapi 0.7.5

  • Moved to STRING database version 11.5

rbioapi 0.7.4

CRAN release: 2021-06-22

  • Bug fixes and minor improvements.

rbioapi 0.7.3

  • Improved internal functions.

rbioapi 0.7.2

  • JASPAR is supported.

rbioapi 0.7.1

  • Enrichr is supported.

rbioapi 0.7.0

CRAN release: 2021-04-30

  • The package was submitted to CRAN