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Changelog

Source: NEWS.md

cinaR 0.2.6

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 2020-11-14

  • cinaR is published in CRAN repository!