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… vignette - Rename calc_jaccard() to geneset_similarity() across all R sources - Rename vignettes/pathway_analysis_clustering.Rmd to PA_clustering.Rmd - Regenerate documentation via devtools::document()
- Configure GitHub Pages via usethis::use_pkgdown_github_pages()
- Add URL to DESCRIPTION pointing to BigMindLab GitHub Pages - Add example datasets section to reference index in _pkgdown.yml - Fix GitHub icon aria-label
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Summary
This PR finalizes the PA Clustering module and sets up the pkgdown documentation site.
Changes
Refactor
calc_jaccard()→geneset_similarity()across all R sources(
R/dataclust_PA.R,R/doclust_PA.R,R/list_gmts.R,R/plotclust_PA.R,data-raw/example_PA.R)vignettes/pathway_analysis_clustering.Rmd→vignettes/PA_clustering.Rmddevtools::document()Documentation site
_pkgdown.ymlwith full site configuration:#6000C6)usethis::use_pkgdown_github_pages()URLtoDESCRIPTIONpointing tohttps://bigmindlab.github.io/OmicsKit.Rbuildignoreand.gitignoreaccordinglyNotes
gh-pagespkgdown::deploy_to_branch()to publish the site