LoginSign Up
← Back to all sparks
G

grex

ANALYTICS
Velocity0.0

Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data

github.com/nanxstats/grex ↗

grex is a lookup table with a version number — it ships when the annotation moves.

gtexgene-annotationbioinformaticsreference-datamaintenance-mode
◆Current state
grex converts the deprecated Ensembl gene IDs found in GTEx data into current gene symbols and identifiers, using org.Hs.eg.db as its reference. Its value is entirely in that bundled reference data, so a release either refreshes the mapping or does nothing to it. The 2025 release does nothing to it: GitHub Actions for the docs site, a check-note fix, and a smaller vignette.
◆Where it's heading
The annotation refreshes stopped. Between 2017 and 2019 the package tracked org.Hs.eg.db through four versions and added the GTEx V7 identifier set; since then the reference has stood still while the releases turned to packaging. That gap matters more here than it would elsewhere — a stale mapping table silently returns outdated symbols rather than failing, so the package's core asset ages invisibly.
◆Prediction
Nothing in these entries signals a planned data refresh, and the six-year pattern suggests the next release will again be infrastructure. Users needing current annotations should check which org.Hs.eg.db version is bundled rather than assume the version number reflects it.

◆Recent moves

  1. 1y ago

    grex 1.9.1: pkgdown on Actions, smaller vignette

    Packaging only — the docs site moves to GitHub Actions, r-devel file URI notes are cleared, and the vignette switches to html_vignette to shrink the package. Notably the reference database is untouched, as it has been since 2019. Ships the same day as sibling package enpls with the same two fixes.

    View source ↗
  2. 7y ago

    grex 1.9 refreshes the reference to org.Hs.eg.db 3.8.2

    The last annotation refresh the package has had. For a mapping table this is the substantive kind of release — the identifiers users get back change — even though the note reads like housekeeping.

    View source ↗
  3. 8y ago

    grex 1.8 adds GTEx V7 IDs, updates to org.Hs.eg.db 3.6.0

    A new gtexv7 dataset joins the bundled identifier sets alongside a reference refresh. Adding a GTEx release version is the clearest signal of the package doing its actual job: keeping pace with the data source it exists to translate.

    View source ↗
  4. 8y ago

    grex 1.7 updates the reference to org.Hs.eg.db 3.4.2

    A single-line release that bumps the bundled annotation. Routine at the time, and part of the once-or-twice-a-year cadence the package has since abandoned.

    View source ↗
  5. 8y ago

    grex 1.6 drops Google Fonts from vignettes

    A system font stack replaces Google Fonts to work around a pandoc SSL problem. Build-environment plumbing with no effect on the mappings.

    View source ↗
  6. 9y ago

    grex 1.5 adds a pkgdown site and refreshes the reference

    A documentation website plus an org.Hs.eg.db 3.4.1 refresh — the combination that characterized the package's active period, when packaging work rode along with data updates rather than replacing them.

    View source ↗