Changes in version 0.4.0 (2026-07-25)                  

CRAN Resubmission

  - Bundled real data files in data/ (tcga, icgc, pcawg_full,
    pcawg_simple) instead of empty placeholders — core functions now
    work fully offline.
  - load_data() now loads bundled datasets directly via utils::data(),
    falling back to Zenodo download only for non-bundled data.
  - Added LazyDataCompression: xz to DESCRIPTION to comply with CRAN
    policy for lazy data larger than 1 MB.
  - Wrapped parse_gdc_file_uuid() examples in \dontrun{} to prevent
    network access during R CMD check.
  - ls_annotables() and convert_hm_genes() now handle offline state
    gracefully with informative messages.
  - Updated Zenodo record URL from 6342397 to 10360995 (/records/
    format).
  - Added biocViews: field to DESCRIPTION for Bioconductor
    compatibility.

New Features

  - Added build_annotables() — builds up-to-date gene annotation tables
    directly from Ensembl BioMart using recipes from the annotables
    package. Supports 11 organisms (including dog, zebrafish, pig) with
    mirror fallback and local caching. Requires biomaRt (Bioconductor).
  - Added pair_gdc_samples() — pairs tumor-normal samples from GDC
    manifest files. Automatically classifies tumor vs normal by TCGA
    barcode, prefers blood-derived normals, and generates all
    tumor-normal combinations per case. (#7)
  - convert_hm_genes() now supports ce11 (C. elegans) and T2T (human
    T2T/CHM13) genome builds.
  - Added resolve_gene_aliases() — resolves outdated or alternative gene
    symbols (e.g., "MLL" -> "KMT2A") using Ensembl synonym data.
    Requires build_annotables(include_synonyms = TRUE) for source data.
    (#11)
  - build_annotables() gains include_synonyms parameter to fetch
    external_synonym from Ensembl BioMart.
  - Added convert_hm_orthologs() — converts gene symbols or Ensembl IDs
    between human and mouse via Ensembl orthology (e.g., TP53 <->
    Trp53). Supports high-confidence filtering and cached queries.

Other Changes

  - Repository migrated from ShixiangWang/IDConverter to
    WangLabCSU/IDConverter. All URLs updated in DESCRIPTION, README,
    pkgdown config, and documentation.
  - All Rd files regenerated via devtools::document() for consistency.
  - Added IDConverter.Rcheck/ to .gitignore and .Rbuildignore.

                        Changes in version 0.3.5                        

  - Removed from CRAN.
  - Removed hard code of the .data_path in the package.

                 Changes in version 0.3.4 (2023-03-14)                  

  - Suppressed the check warning and error.

                 Changes in version 0.3.3 (2022-08-15)                  

  - Printed more reasonable message when network is not available.

                 Changes in version 0.3.2 (2022-06-03)                  

  - Enhanced parse_gdc_file_uuid().

                        Changes in version 0.3.1                        

  - Re-implemented parse_gdc_file_uuid().

                 Changes in version 0.3.0 (2022-03-11)                  

  - Used tempdir as user default data directory.
  - Supported annotables annotation data tables by combining newly
    created ls_annotables() and load_data().
  - Added convert_hm_genes() - Convert human/mouse gene IDs between
    Ensembl and Hugo Symbol system.

                 Changes in version 0.2.0 (2022-03-09)                  

  - Added filter_tcga_barcodes for TCGA barcode filtering.
  - Moved all data to Zenodo https://zenodo.org/record/6336671 to keep
    this package smaller.

                        Changes in version 0.1.1                        

  - Added parse_gdc_file_uuid() to "Parse Metadata from GDC Portal File
    UUID".
  - Added multiple option to return a map data.table.

                        Changes in version 0.1.0                        

  - Added convert_custom() to allow user construct custom database for
    conversion.
  - Added convert_icgc().
  - Added convert_pcawg().
  - Added convert_tcga().

                     Changes in version 0.0.0.9000                      

  - Added a NEWS.md file to track changes to the package.