NEWS

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cinaR 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

cinaR 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

cinaR 0.2.4

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

cinaR 0.2.3 (2022-05-18)

• Minor improvements

cinaR 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.

cinaR 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.

cinaR 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.

cinaR 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

cinaR 0.1.0 (2020-11-14)

• cinaR is published in CRAN repository!