# DOtools 1.1.8

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

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## [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.


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## [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`

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## [0.99.5] - 2025-09-30

### Changed
* Major coding adjustments for preparing BioConductor release

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## [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.

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## [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.

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## [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.

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## [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.

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## [0.1.1] - 2025-05-26

### Changed
* Minor adjustments to function behavior and formatting.

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## [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.

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## [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.

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## [0.0.1] - 2025-03-27

### Added
* Initial commit: core structure and foundational functions.
