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- DESCRIPTION: Rewrite Title/Description, add biocViews, URL, BugReports, VignetteBuilder, bump R >= 4.4.0, add BiocStyle/knitr/rmarkdown to Suggests - Add BiocStyle vignette (vignettes/ribiosExpression.Rmd) - Convert NEWS to NEWS.md - Add @return tags to all exported generics and functions - Fix typos (annotaiton, suing, coereced, DesignContras, feta.name) - Replace class(x) %in% with is.numeric() - Replace 1:length()/1:ncol()/1:nlevels() with seq_len()/seq_along() - Replace subset()/with() with direct $ indexing in truncateDgeTable - Remove internal Roche wiki URL from documentation - Update http to https for Broad Institute URLs - Fix positional argument in writeGct eSet method - Remove duplicate @exportMethod on setter generics - Add @Format and @examples to data documentation - Update .Rbuildignore
- Update standard-ci-workflow.yml to use actions/checkout@v4, r-lib/actions@v2 - Replace deprecated ubuntu-16.04 with ubuntu-latest - Add macOS devel and ubuntu oldrel-1 to test matrix - Add pkgdown.yaml workflow for documentation site generation - Add .github/.gitignore Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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