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Update Ensembl annotation workflow, tests, and vignettes #44

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Merged
DanielGarbozo merged 7 commits into from
May 6, 2026
Merged

Update Ensembl annotation workflow, tests, and vignettes #44

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156d891
Merge pull request #43 from BigMindLab/dev
DanielGarbozo Apr 25, 2026
6e17702
Refactor get_annotations, add Ensembl helpers
DanielGarbozo May 5, 2026
cf06252
Update DEA-workflow vigenette
DanielGarbozo May 5, 2026
d56ba18
Update PA-workflow and rebuild vignettes
DanielGarbozo May 5, 2026
c1c1ebc
fix: [testthat/test-get_annotation.R] use specific Ensembl host in sk…
DanielGarbozo May 5, 2026
6214f42
fix: set stable version on get_annotation tests
DanielGarbozo May 5, 2026
d5e5309
fix: eval=FALSE while get_annotation used in PA_workflow.Rmd
DanielGarbozo May 6, 2026
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4 changes: 4 additions & 0 deletions .Rbuildignore
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Expand Up @@ -8,3 +8,7 @@
^_pkgdown\.yml$
^docs$
^pkgdown$
^\.positai$
^\.claude$
^doc$
^Meta$
3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -53,3 +53,6 @@ rsconnect/
.quarto
inst/doc
docs
.positai
/doc/
/Meta/
8 changes: 5 additions & 3 deletions DESCRIPTION
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Expand Up @@ -55,12 +55,14 @@ Suggests:
tidygraph,
tidyr,
tidyselect,
tm
tm,
testthat (>= 3.0.0),
withr
Roxygen: list(markdown = TRUE)
Depends:
R (>= 3.5)
R (>= 4.4.0)
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
URL: https://bigmindlab.github.io/OmicsKit

Config/testthat/edition: 3
2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -12,6 +12,8 @@ export(get_superterm)
export(getgenesPA)
export(heatmap_PA)
export(heatmap_path_PA)
export(list_ensembl_species)
export(list_ensembl_versions)
export(list_gmts)
export(merge_PA)
export(multiplot_PA)
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