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Changelog

Source: NEWS.md

Version 2.3.0

  • Updated NCI Thesaurus (26.04d)
  • Updated CIViC data (20260529)
  • Updated Mitelman database (20260415)
  • Updated OTP (2026.03)
  • New vignette in quarto format + reactable tables

Version 2.2.6

  • Updated CIViC data (20260323)

Version 2.2.5

  • Updated NCI Thesaurus (2026.02d)
  • Updated CIViC data (20260320)

Version 2.2.3

  • Make uniform ordering of biomarker-associated therapies

Version 2.2.2

  • Fixed some biomarker drug names

Version 2.2.1

  • Fixed mapping of fusion partner entrez gene identifiers

Version 2.1.9

  • CIViC update (20260216)
  • NCI Thesaurus update (26.01d)

Version 2.1.8

  • CIViC update (20260119)
  • MitelmanDB update (20260115)

Version 2.1.7

  • CIViC update (20260101)

Version 2.1.6

  • Open Targets Platform update (2025.12)
  • CIViC update (20251210)

Version 2.1.5

  • NCI Thesaurus update (2025.11d)
  • CIViC update (20251204)

Version 2.1.4

  • NCI Thesaurus update (2025.10d)
  • CIViC update (20251109)

Version 2.1.2

  • NCI Thesaurus update (2025.09e)
  • CIViC update (20251103)

Version 2.0.0

  • Fixed missing drug classifications for some drugs
  • Updated phenOncoX for more drug indications

Version 1.9.8

  • NCI Thesaurus update (2025.08d)
  • CIViC update (20250910)

Version 1.9.7

  • NCI Thesaurus update (2025.07d)
  • CIViC update (20250807)
  • MitelmanDB update (20250715)
  • Open Targets Platform update (2025.06)

Version 1.9.5

  • NCI Thesaurus update (2025.04d)
  • CIViC update (20250531)

Version 1.9.4

  • Open Targets Platform update (25.03)
  • NCI Thesaurus update (2025.03e)
  • CIViC update (20250501)
  • MitelmanDB update (20250410)

Version 1.9.3

  • CIViC update (20250313)
  • NCI Thesaurus update (2025.02d)

Version 1.9.1

  • CIViC update (20250207)
  • NCI Thesaurus update (25.01d)

Version 1.9.0

  • CIViC update (20250127)
  • MitelmanDB update (20250115)

Version 1.8.8

  • Removed buggy drug aliases from PubChem
  • Updated DepMap RNA fusion events (24Q4)

Version 1.8.7

  • NCI Thesaurus update (24.11d)
  • CIViC update (20241218)
  • New custom drug categories
    • ICIs - CTLA4 inhibitors
    • ICIs - TIGIT inhibitors
    • ICIs - LAG3 inhibitors

Version 1.8.1

  • CIViC update (20241107)
  • NCI Thesaurus update (24.10d)

Version 1.8.0

  • CIViC update (20241102)
  • NCI Thesaurus update (24.09e)
  • OTP update (2024.09)
  • Clean-up of code for ChEMBL drug mappings
    • skip DGIdb cross-references - rely on OTP

Version 1.7.3

  • CIViC update (20240918)

Version 1.7.2

  • CIViC update (20240904)

Version 1.7.1

  • CIViC update (20240826)
    • added location of MET exon 14 skipping splice site (grch37 principal transcript)

Version 1.7.0

  • CIViC update (20240807)
  • NCI Thesaurus update (24.07e)
  • MitelmanDB update (20240715)
  • New dataset: DepMap (cell line) RNA fusion events

Version 1.6.10

  • Fixed some erroneous drug classifications
  • CIViC update (20240621)
  • OTP update (2024.06)

Version 1.6.8 (June 7th 2024)

  • NCI Thesaurus update (24.05d)

Version 1.6.7 (May 23rd 2024)

  • NCI Thesaurus update (24.04e)
  • CIViC update (20240523)

Version 1.6.4 (April 30th 2024)

  • Improved clinical (tumor site) annotations of fusions from MitelmanDB

Version 1.6.3 (April 26th 2024)

  • CIViC update (20240426)

Version 1.6.2 (April 12th 2024)

  • NCI Thesaurus update (24.03d)

Version 1.6.1 (March 26th 2024)

  • Open Targets Platform update (v2024.03)

Version 1.6.0 (March 9th 2024)

  • CIViC/Mitelmandb updates

Version 1.5.9 (February 29th 2024)

  • Updated CIViC

Version 1.5.8 (February 6th 2024)

  • NCI Thesaurus update (24.01e)

Version 1.5.7 (February 3rd 2024)

  • Fixed buggy alias from PubChem

Version 1.5.6 (January 31st 2024)

  • Refine possible values in treatment_category argument to get_drugs() function
  • Fix anti-androgen classification
  • Fixed bug in alias type notation for copy numbers and expression biomarkers
  • Filter noise and rank output in helper function get_targeted_drugs
  • Include variant primary name in biomarker variants

Version 1.5.0 (January 25th 2024)

  • Considerable improvement of drug classifications (output column atc_level3), considering both targeted agents and chemotherapy
  • argument drug_targeted_agent renamed to treatment_category
  • helper function get_on_off_label_drugs renamed to get_targeted_drugs

Version 1.4.10 (January 17th 2024)

  • Updated NCI Thesaurus (23.12d)
  • Updated CIViC data (20240114)
  • Revised manual drug classification (building upon ATC)

Version 1.4.8 (December 12th 2023)

  • Updated NCI Thesaurus - 23.11d
  • Updated CIViC data (20231212)

Version 1.4.8 (November 30th 2023)

  • Updated OTP (v2023.12)
  • Updated Mitelman database (20231016)

Version 1.4.7 (November 3rd 2023)

  • Fixed corrupt biomarker literature data frame

Version 1.4.6 (October 18th 2023)

  • Fixed metadata
  • Fixed out-dated version descriptions (GH site)
  • Do not exclude compounds with missing drug action type (platins etc.)

Version 1.4.5 (October 6th 2023)

  • Updated NCI Thesaurus - 23.09d
  • Updated CIViC data
  • Added drug class (ATC) to get_on_off_label_drugs()

Version 1.4.4 (September 1st 2023)

  • Updated NCI Thesaurus - 23.08d
  • Updated CIViC data
  • Updated Mitelman database (20230803)
  • get_biomarkers() now exported as a main function