- Support for GENCODE v46
- CGC v100
- make gene biotype more uniform across GENCODE builds
- Added more gene aliases (one edit distance away from existing aliases, found as substrings in other genename designations)
- Including references to non-coding RNA identifiers from RefSeq in
refseq_transcript_id
column
- Updated cancer gene ranks from OTP (v24.03)
- Added GENCODE entries for transcripts originating on scaffolds etc. (not just chromosomes)
- Updated NCBI gene info
- Added cancer gene ranks from OTP
- Added support for GENCODE v45
- Updated gene descriptions, and updated helper function
assign_cancer_gene_roles
- 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
- Renamed columns of GENCODE data frame:
refseq_mrna
->refseq_transcript_id
refseq_peptide
->refseq_protein_id
- Removed trailing lines from Genomics England PanelApp phenotype descriptions
- NCBI gene function update
- Helper function
get_cancer_gene_roles
updated
- Grab gene names/descriptions from Ensembl if missing from NCBI
- 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.
- Updated metadata table
- Updated IntOGen
- Fixed hyphens in URLs (CGC, NCG, IntOGen)
- Added licensing terms
- Minor change to column names in cancer predisposition gene records
- Updated Cancer Gene Census (v98)
- Updated gene annotations from dbNSFP (v4.4)
- Updated Network of Cancer Genes (v7.1)
- Updated UniProt (2023_02)
- Retrieved new PanelApp genes (March 2023)
- Upgraded CancerMine (v50, March 2023)
- 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
- Upgraded GENCODE (v43), Ensembl v109
- Fixed a bug in the helper function
assign_cancer_gene_evidence
- Upgraded CancerMine (v49, January 2023)
- Added a few custom gene aliases
- Ensured both primary symbols and aliases were present in the gene alias data frame
- Use tidyverse code style
- Ignore genes from NCBI with biotype
biological-region
- Improved UniProt identifier mappings for Ensembl transcripts associated with the grch37 genome assembly
- Updated CGC (v97)
- 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)
- Updated GENCODE (v42), and NCBI gene info (2022-10-31)
- 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
- Added F1CDx annotation (Foundation One)