NEWS

DOtools 1.1.8

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

[1.1.8] - 2026-04-13

Added

Added citation from Bioinformatics Advances since it got published.

Changed

DO.UMAP: Is now able to plot a DensityPlot for provided genes.

[1.1.2] - 2026-01-13

Added

DO.HeatmapFC: Heat map function for foldchange visualisation, includes statistics about significance.
DO.Barplot: New barplot function with more testing methods.

Changed

Major adjustments to DO.VlnPlot and DO.Barplot. These functions now take multiple testing methods and correction methods. Will be applied also to DO.BoxPlot.
Major bug fixes for comparability with Seurat's newest version.

Removed

DO.BarplotWilcox: Replaced by DO.Barplot

[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.