Changes in version 0.2.6 (2026-02-04)                  

  - Fixed plotting helpers (pheatmap ..., dot-plot scale, PCA palette)
  - Wired norm.method/filter.method into the pipeline
  - Made run_enrichment() more robust to input shape and empty contrasts
  - Added prep_scATAC_seurat() helper for Seurat/Signac objects
  - Added llms.txt and starter MCP JSON schemas for agent integration

                        Changes in version 0.2.5                        

  - Added scATAC preprocessing helper prep_scATAC_cinaR() and vignette
    example
  - Added package citation file and updated preprint URL
  - Guarded annotatePeaks() for missing ChIPseeker
  - Fixed upcoming CRAN checks

                        Changes in version 0.2.4                        

  - Bug fix and changes:
      - Bioconductor related packages are suggested
      - Added .on_attach() for smooth CRAN checks

                 Changes in version 0.2.3 (2022-05-18)                  

  - Minor improvements

                        Changes in version 0.2.2                        

  - Added:
      - comparison.scheme either set to OVO (default) which will compare
        each contrasts to each other. If it's set to OVA each contrast
        will be compared to rest.

                 Changes in version 0.2.1 (2021-04-02)                  

  - Added:
      - An extra argument sv.number is added if user wants to set the
        number of surrogate variables.
        More info here.
      - verbose argument, default set to TRUE. I think, I have
        implemented this in a really cool way!
      - cinaRgenesets added to vignette.

                 Changes in version 0.2.0 (2021-01-05)                  

  - Added:
    
      - heatmap_differential function to be able to plot the heatmaps of
        a given comparison.
      - show_comparisons is added to see the available comparisons
        before you plot differential heatmaps.

  - Changed:
    
      - heatmap_plot is now renamed to heatmap_var_peaks, which makes
        more sense.

                        Changes in version 0.1.1                        

This version is even cooler, lol:

  - Comparisons are now sorted according to contrast order
  - Added bulk RNA-seq support/documentation
  - Removed many dependencies
  - Small bug fixes and improvements

                 Changes in version 0.1.0 (2020-11-14)                  

  - cinaR is published in CRAN repository!