PCGR v.2.0rc - 2024

[sigven]

• Functionality to support new reference data management
• Functionality to support RNA-seq (bulk) expression input - correlation against reference samples (TCGA/DepMap/Treehouse), preliminary outlier detection (TCGA only)
• Functionality to support VEP cache as a separate entity from the PCGR reference data
• New copy number input format - absolute, allele-specific (nMajor + nMinor)
• Copy number annotation moved from pcgrr to Python workflow
• Variant oncogenicity assessment (SNVs/InDels, based on VICC/ClinGen guidelines) implemented in Python workflow
• More robust biomarker matching implemented in Python workflow - considering genomic coordinates, HGVSp entries (considering principal and non-principal matches)
• New HTML templates - quarto-based
• New Excel workbook output

[pdiakumis]

Adding a mini list of remaining TODOs (will update as we go):

• [x] Update r-base to 4.3 (https://github.com/sigven/cpsr/pull/55, https://github.com/sigven/pcgr/pull/227)
• [ ] Update installation documentation
• [ ] Install {CNAqc} with {remotes}
  • There is no conda pkg and it has many dependencies that are not released pkgs, so install with {remotes} directly from GitHub for now (it takes ~20+ minutes unfortunately). We'll try to replace with custom CNA visualiser.
• [ ] Replace {reshape2} dependency
  • substitute reshape2::melt with tidyr::pivot_longer since {reshape2} is deprecated
  • https://github.com/umccr/pcgr/blob/bundle_update_2023/pcgrr/R/mutational_signatures.R#L274
• [ ] Create {openxlsx2} conda pkg
  • This is on CRAN so we'll open a conda-forge PR, should be straightforward. Doing it via remotes for now and it's infinitely less noisy than {CNAqc}.
  • https://github.com/conda-forge/staged-recipes/pull/26497