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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.LazyDataCompression: xz to DESCRIPTION to comply
with CRAN policy for lazy data larger than 1 MB.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./records/ format).biocViews: field to DESCRIPTION for Bioconductor
compatibility.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).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elegans) and T2T (human T2T/CHM13) genome builds.resolve_gene_aliases() — resolves outdated or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.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.ShixiangWang/IDConverter to
WangLabCSU/IDConverter. All URLs updated in DESCRIPTION,
README, pkgdown config, and documentation.devtools::document() for
consistency.IDConverter.Rcheck/ to .gitignore
and .Rbuildignore..data_path in the
package.parse_gdc_file_uuid().parse_gdc_file_uuid().ls_annotables() and load_data().convert_hm_genes() - Convert human/mouse gene IDs
between Ensembl and Hugo Symbol system.filter_tcga_barcodes for TCGA barcode
filtering.https://zenodo.org/record/6336671 to keep this package
smaller.parse_gdc_file_uuid() to “Parse Metadata from GDC
Portal File UUID”.multiple option to return a map
data.table.convert_custom() to allow user construct custom
database for conversion.convert_icgc().convert_pcawg().convert_tcga().NEWS.md file to track changes to the
package.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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