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Feature/dea functions#40

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DanielGarbozo merged 6 commits intoBigMindLab:devfrom
DanielGarbozo:feature/DEA-functions
Mar 22, 2026
Merged

Feature/dea functions#40
DanielGarbozo merged 6 commits intoBigMindLab:devfrom
DanielGarbozo:feature/DEA-functions

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feat: add DEA workflow, example datasets, and improve function documentation

New vignette:

  • DEA_workflow.Rmd: full RNA-seq DEA workflow with pre-rendered figures
  • prerender_figures.R: script to regenerate vignette figures
  • vignettes/figures/: pre-rendered PNG plots (power, PCA, UMAP, tSNE, Volcano, VSB)

Documentation improvements (all functions):

  • Add @return, @Seealso, @note to all DEA functions
  • Add @references to nice_UMAP, nice_tSNE.
  • Update @param label_var in nice_Volcano and @param symbol in nice_VSB
    to mention get_annotations() for symbol-based labeling
  • Add note for nice_VSB_DESeq2 alternative in DEA vignette

Bug fixes:

  • get_annotations: fix rowNames → row.names in write.csv
  • save_results: add underscore separator and include l2fc/cutoff_alpha
    values in output filenames for traceability
  • power_analysis: return $plot slot in output list; plot built
    conditionally only when plot = TRUE

Other:

  • Update DESCRIPTION: LazyDataCompression xz, DESeq2 to Suggests
  • Update .Rbuildignore: exclude vignettes/prerender_figures.R
  • Update NAMESPACE and man/

- 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)
- Add underscore separator before up/down in output filenames
- Include l2fc and cutoff_alpha values in filename for traceability
- Update @return, @examples, and DEA vignette accordingly
- Fix get_annotations: replace rowNames with row.names in write.csv
@DanielGarbozo DanielGarbozo merged commit 99b5100 into BigMindLab:dev Mar 22, 2026
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