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NEWS.md

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rbioapi 0.8.2 (Current CRAN version)

  • 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

  • Move to JASPAR 2024.

  • Minor improvements and fixes.

rbioapi 0.8.0

  • Move to STRING v12.

  • Incorporate the recent changes in PANTHER and MIEAA API.

  • Minor improvements and fixes.

rbioapi 0.7.9

  • Stability improvements.

rbioapi 0.7.8

  • Bug fixes and minor improvements.

rbioapi 0.7.7

  • Bug fixes and minor improvements.

rbioapi 0.7.6

  • 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

  • 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

  • The package was submitted to CRAN