Changes in version 0.5.0.9000                      

                 Changes in version 0.5.0 (2025-12-22)                  

Major Changes

  - added support for gene-level SCNA data frames to be used as input
    for create_features_df() and added an example gene-level SCNA data
    frame example_gene_scna_table

Minor changes and bug fixes

  - Moved org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene and
    TxDb.Hsapiens.UCSC.hg38.knownGene from "Imports" to "Suggests" per
    new CRAN policy. Relevant functions raise error if the required
    package is not installed.

                 Changes in version 0.4.1 (2023-08-19)                  

Minor changes and bug fixes

  - fixed a CRAN error due to a package documentation issue (#7)

                 Changes in version 0.4.0 (2022-08-15)                  

Major Changes

  - Added GRCh38 support

                 Changes in version 0.3.0 (2022-01-18)                  

Major Changes

  - Updated the cancer-type-specific thresholds

Minor changes and bug fixes

  - Updated citation to the method's article where necessary

                 Changes in version 0.2.1 (2020-11-25)                  

Major Changes

  - Updated the MTL model after fixing the issue below
  - Fixed issue in MCR_table. The coordinates were converted to hg19
    (from hg18)

Minor changes and bug fixes

  - Made use of caret::predict.train explicit
  - Removed 'Homo.sapiens' from Imports field (not used)

                 Changes in version 0.2.0 (2020-11-19)                  

Major Changes

  - Fixed an issue in create_SCNA_score_df() where the SCNA score was
    not calculated because the column name for "MCR_overlap_percent" was
    incorrectly assigned as "transcript_overlap_percent"
  - Updated the MTL classification model TCGA_MTL_fit and
    specific_thresholds after fixing the issue above

Minor changes and bug fixes

  - Updated citation information, correcting author name
  - Minor changes in utility functions
  - Added the na.string argument to create_noncoding_impact_score_df(),
    predict_coding_impact() and create_features_df() as the string that
    was used to indicate when a score is not available during annotation
    with ANNOVAR (default = ".")
  - Generalized determine_hotspot_genes() to able to use occurrence
    annotations from different versions of COSMIC
  - Updated all data

                 Changes in version 0.1.1 (2020-11-18)                  

Initial release