IDConverter 0.4.0

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• Added resolve_gene_aliases() — resolves outdated or alternative gene symbols (e.g., “MLL” -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.

IDConverter 0.3.5

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

IDConverter 0.3.4

• Suppressed the check warning and error.

IDConverter 0.3.3

• Printed more reasonable message when network is not available.

IDConverter 0.3.2

• Enhanced parse_gdc_file_uuid().

IDConverter 0.3.1

• Re-implemented parse_gdc_file_uuid().

IDConverter 0.3.0

• 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.

IDConverter 0.2.0

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

IDConverter 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.

IDConverter 0.1.0

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

IDConverter 0.0.0.9000

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