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Changelog

Source: NEWS.md

Version 1.0.0

  • Updated IntOGen (v2024.10)
  • Updated NCBI summary information
  • Updated GENCODE to v47
  • moved from bump2version (deprecated) to bump-my-version

Version 0.9.9

  • Updated NCBI gene information
  • Added cds_start to GENCODE transcripts

Version 0.9.7

  • fixed bug in Entrez gene identifiers (grch37)
  • fixed bug in HGNC id map (grch38)
  • added missing Entrez gene identifiers (grch37/grch38)
  • added missing names for genes (grch37/grch38)

Version 0.9.2

  • GENCODE transcript tracks:
    • Pull in more up-to-date MANE select transcripts from NCBI
    • Pull in RefSeq Select identifiers (grch37)
    • Use exact version numbers for transcripts/MANE select.

Version 0.9.1

  • Use up-to-date gene symbols from NCBI in GENCODE tracks, ignore outdated Entrez gene identifiers from BioMart

Version 0.9.0

  • Update NCBI gene information

Version 0.8.10

  • Support for GENCODE v46

Version 0.8.9

  • CGC v100
  • make gene biotype more uniform across GENCODE builds

Version 0.8.6

  • Added more gene aliases (one edit distance away from existing aliases, found as substrings in other genename designations)

Version 0.8.5

  • Including references to non-coding RNA identifiers from RefSeq in refseq_transcript_id column

Version 0.8.3

  • Updated cancer gene ranks from OTP (v24.03)
  • Added GENCODE entries for transcripts originating on scaffolds etc. (not just chromosomes)

Version 0.8.1

  • Updated NCBI gene info

Version 0.8.0

  • Added cancer gene ranks from OTP

Version 0.7.14

  • Added support for GENCODE v45

Version 0.7.13

  • Updated gene descriptions, and updated helper function assign_cancer_gene_roles

Version 0.7.12

  • New panel from PanelApp included in cancer panels and included in list of cancer predisposition genes: Inherited susceptibility to acute lymphoblastoid leukaemia (ALL) (GEP)
  • Updated Cancer Gene Census to v99

Version 0.7.11

  • Renamed columns of GENCODE data frame:
    • refseq_mrna -> refseq_transcript_id
    • refseq_peptide -> refseq_protein_id

Version 0.7.10

  • Removed trailing lines from Genomics England PanelApp phenotype descriptions

Version 0.7.9

  • NCBI gene function update
  • Helper function get_cancer_gene_roles updated

Version 0.7.8

  • Grab gene names/descriptions from Ensembl if missing from NCBI

Version 0.7.6

  • Allowing the possibility to query and retrieve different versions of GENCODE transcripts (using Ensembl version 110 to 105, effectively querying GENCODE v44 to GENCODE v39). This will only effect grch38, for grch37, GENCODE v19 will always be used.

Version 0.7.5

  • Updated metadata table

Version 0.7.4

  • Updated IntOGen
  • Fixed hyphens in URLs (CGC, NCG, IntOGen)
  • Added licensing terms

Version 0.7.3

  • Minor change to column names in cancer predisposition gene records

Version 0.7.2

  • Updated Cancer Gene Census (v98)
  • Updated gene annotations from dbNSFP (v4.4)
  • Updated Network of Cancer Genes (v7.1)
  • Updated UniProt (2023_02)

Version 0.7.1

  • Retrieved new PanelApp genes (March 2023)

Version 0.7.0

  • Upgraded CancerMine (v50, March 2023)

Version 0.6.9

  • Implemented new helper function assign_cancer_gene_roles
    • adds confidence support for tumor supressive/oncogenic roles of genes based on amount of literature evidence and manual curation status

Version 0.6.8

  • Upgraded GENCODE (v43), Ensembl v109

Version 0.6.7

  • Fixed a bug in the helper function assign_cancer_gene_evidence

Version 0.6.6

  • Upgraded CancerMine (v49, January 2023)
  • Added a few custom gene aliases

Version 0.6.5

  • Ensured both primary symbols and aliases were present in the gene alias data frame

Version 0.6.4

  • Use tidyverse code style
  • Ignore genes from NCBI with biotype biological-region

Version 0.6.3

  • Improved UniProt identifier mappings for Ensembl transcripts associated with the grch37 genome assembly
  • Updated CGC (v97)

Version 0.6.2

  • Added a few curated cancer predisposition genes (contributed by UMCCR)
  • Updates from NCBI gene info (2022-11-28)
  • Updated cross-references from UniProt KB (2022_04)

Version 0.6.1

  • Updated GENCODE (v42), and NCBI gene info (2022-10-31)

Version 0.6.0

  • Added a NEWS.md file to track changes to the package.
  • Added geneOncoX.Rmd to vignettes - getting started guide
  • Updated code and documentation according to style recommendations

Version 0.5.5

  • Added F1CDx annotation (Foundation One)