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resolve_gene_aliases() — resolves outdated or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.