Add diabetic nephropathy and urothelial cancer case study vignettes#4

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Copilot wants to merge 6 commits intomainfrom

copilot/add-diabetic-nephropathy-vignette

Commits on Jan 14, 2026

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Add two comprehensive case study vignettes for diabetic nephropathy and urothelial cancer

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ShixiangWang
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Add ggplot2 and tidyr to Suggests for new vignettes

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ShixiangWang
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Address code review feedback: fix date extraction, improve tempdir() documentation, and simplify missing value calculation

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ShixiangWang
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Fix tibble dependency issue and improve date extraction method to use GSE number as time proxy

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ShixiangWang
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Improve backward compatibility by replacing dplyr::if_any() with grepl() and using size instead of linewidth

Copilot
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ShixiangWang
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