Changes in version 0.99.5                        

All notable changes to DOtools will be documented in this file.

[0.99.5] - 2025-09-30

Changed

  - Major coding adjustments for preparing BioConductor release

[0.99.0] - 2025-07-08

Added

  - DO.Heatmap: Heat map function for gene expression, includes
    statistics about significance.
  - Example data set, useable for running the tutorial.

Changed

  - Major adjustments across various functions for improved consistency.
  - Major adjustments across various examples.

[0.4.0] - 2025-06-09

Added

  - DO.SplitBarGSEA: Bar plot function for GSEA results (e.g., from
    Metascape).
  - DO.scVI: Wrapper function to run scVI integration on a Seurat
    object.

Changed

  - Minor adjustments across various functions for improved consistency.

[0.3.0] - 2025-05-28

Added

  - DO.Import: Simplifies Seurat object creation.
  - DO.CellBender: Enables running CellBender on aligner-generated HDF5
    files.

Changed

  - Minor adjustments and internal improvements.

[0.2.0] - 2025-05-26

Added

  - DO.CellBender: Functionality to run CellBender (initial version).
  - DO.BarcodeRanks: New function for barcode rank visualization.

Changed

  - Minor adjustments for stability and usability.

[0.1.1] - 2025-05-26

Changed

  - Minor adjustments to function behavior and formatting.

[0.1.0] - 2025-04-09

Added

  - DO.CellCompositions: Integrates the scanpro tool to detect changes
    in cell composition.
  - New connected stacked bar plot in scanpro output highlighting
    significant composition changes.
  - DO.Dotplot: Added pseudobulk option for y-axis.

[0.0.2] - 2025-04-03

Fixed

  - Bug in DO.Box.plot: Meta.data features could not be specified.
  - Bug in DO.Vln.plot: Meta.data features could not be specified.

Added

  - New argument in DO.Box.plot: Enables user-defined x-axis sorting.

[0.0.1] - 2025-03-27

Added

  - Initial commit: core structure and foundational functions.