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- Add vignettes/DEA_workflow.Rmd: full DEA workflow vignette - Add vignettes/prerender_figures.R: script to generate figures - Add vignettes/figures/: pre-rendered PNG plots - Update @param in nice_Volcano, nice_VSB_DESeq2 and nice_VSB with get_annotations() tip - Add note for nice_VSB_DESeq2 in vignette
…ript - Add slot to power_analysis() return list if plot=TRUE - Update vignettes/prerender_figures.R to use result_power directly instead of rebuilding the ggplot from scratch
- nice_PCA, nice_UMAP, nice_tSNE, nice_Volcano, nice_VSB, nice_KM - power_analysis, get_annotations, add_annotations, tpm - detect_filter, get_stars, save_results, split_cases - Add @references for UMAP, tSNE, and TPM methods - Add @note to get_annotations (gene_length caveat) and tpm (DEA warning)
- Fix get_annotations: replace rowNames with row.names in write.csv
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feat: add DEA workflow, example datasets, and improve function documentation
New vignette:
Documentation improvements (all functions):
to mention get_annotations() for symbol-based labeling
Bug fixes:
values in output filenames for traceability
conditionally only when plot = TRUE
Other: