Changes in version 1.9.1 (2021-10-16)
+ depecheCoFunction updated to remove traces of the old dAllocate functionality

Changes in version 1.7.2 (2021-03-25)
+ Major internal changes to the depeche function, with two user consequences:
    o The dualDepeche option is deprecated, as it made the function very heavy
    to maintain and was not flexible enough to be of great use. 
    o The interface to dAllocate is much improved, allowing for smooth 
    allocation of new data to an established model, which makes large 
    dualDepeche runs, constructed outside of the function, possible in a more
    versatile way than previously.

Changes in version 1.7.1 (2021-02-02)
+ Adding the option of not scaling the data within the depeche function
+ Condensing the code for the depeche scaling procedure

Changes in version 1.5.4 (2020-09-17)
+ Correction of the information about the content of the output from depeche.

Changes in version 1.5.3 (2020-07-02)
+ Correcting the p-adjustments, so that it in fact uses Benjamini-Hochberg, and
+ not the more conservative Hochberg, as default.

Changes in version 1.5.2 (2020-06-05)
+ Introducing samplingSubset in the depeche function
+ Bug fixes in dOptPenalty
+ Small text updates to main vinjette and examples, without code implications.

Changes in version 1.5.1 (2020-05-18)
+ Introduction of neighSmooth - a generalization of groupStatPlot. 
+ Bug fix and simplification of dOptPenalty termination criteria. 
+ Re-tidying of the code base. 

Changes in version 1.3.3 (2020-03-18)
+ Hiearchical clustering and ordering of the columns in the Cluster_centers 
  heatmap from depeche.
+ Note fixed regarding the use of ::: in GroupStatPlot

Changes in version 1.3.2 (2020-02-05)
+ Bug fix in groupProbPlot solving issues when the cell number is low. 
+ Update of dWilcox. 
    
Changes in version 1.3.1 (2019-12-05)
+ Vinjette changes
    o Introduction of a vinjette for the groupProbPlot function.
    o Fixing a minor bug in the general vinjette. 
    
Changes in version 1.1.9 (2019-10-06)
+ Two changes making package more BioConductor compliant: 
    o Introduction of a "Installation" and a "Session info" slot in the vinjette
    o Formatting change of this NEWS file. 

Changes in version 1.1.8 (2019-09-12)
+ Bug fixes. True also for last version.  

Changes in version 1.1.6 (2019-09-12)
+ Adding export option for the vector created by groupProbPlot 
+ Correcting dColorPlot so that it can take a hex color vector as input, and
+ keep the colors. 
+ Adding a test for groupProbPlot.
+ Minor bug fixes for groupProbPlot.
+ Small edits to the vinjette, to clarify that umap is preferred over tSNE and
+ that dViolins currently does not fully support plotting of CyTOF data due to
+ its sparsity. 

Changes in version 1.1.5 (2019-08-07)
+ 4x speedup of the new groupProbPlot. 
+ Proper citations of the MixOmics package, that the dSplsda function uses 
+ heavily. 
+ Bug fixes of the groupProbPlot. 

Changes in version 1.1.4 (2019-07-30)
+ A brand new function is added! Here, the user can get single-cell resolution
+ on which group of two that a cell is more probable to belong to. See docs for 
+ further information. Highly recommended to test!
+ Internal c++ test corrected by external contribution by Zimoun, which we are 
+ most grateful for. 

Changes in version 1.1.3 (2019-06-28)
+ dResidualPlot bug making colors sometimes represent the wrong group fixed.

Changes in version 1.1.2 (2019-06-28)
+ Fixing the dColorPlot and the dDensityPlot functions, so that original names 
+ in character vectors and factors are correctly displayed.


Changes in version 0.99.31 (2019-03-13)
+ dColorPlot and dDensity plot simplified, in that it is now possible to add
+ just a vector of any kind, and it will be returned as colors. 
+ A colorScale alternative, linking to dColorVector has been added to the above.
+ A new legend has been added to dColorPlot. 
+ The options createDirectory and directoryName have been removed from all 
+ visualization functions and have been replaced by plotDir. 
+ The different "name" arguments for plots have been streamlined to be called
+ plotName in all instances, to avoid using base function names for objects.
+ The testData dataset has been made smaller, to increase example execution time
+ and diminish pacakge size.
+ dViolins completely worked over. Now, assymetrical violin plots are generated, 
+ leading to a more succinct result. 
+ Responses to all issues raised by BioConductor reviewer.
+ Bug fix in dual depeche

Changes in version 0.99.30 (2019-02-18)
+ dViolins completely worked over. Now, assymetrical violin plots are generated, 
+ leading to a more succinct result. 
+ Responses to all issues raised by BioConductor reviewer.
+ Bug fix in dual depeche

Changes in version 0.99.24 (2019-01-24)
+ Technical, internal tests have been made more efficient. 
+ Redundant and time consuming examples have been given a dontrun command. 
+ No changes to user functions. 

Changes in version 0.99.20 (2019-01-23)
+ Selecting the number of used cores made more Windows-friendly.

Changes in version 0.99.13 (2019-01-18)
+ Package size made considerably smaller.

Changes in version 0.99.9 (2019-01-15)
+ The figure files connected to the vinjette have been moved out of the package 
+ to a separate github directory. This will reduce the package size 
+ significantly.

Changes in version 0.99.3 (2019-01-15)
+ No errors or warnings in BiocCheckGitClone after removal of .Rapp.history 

Changes in version 0.99.1 (2019-01-14)
+ C++ code reorganized, making package considerably smaller after build. 
+ Package now passes both CMD check and BiocCheck without errors or warnings.

Changes in version 0.81.4 (2019-01-11)
+ Multicore feature made functional for dColorPlot, increasing execution speed. 

Changes in version 0.81.3 (2019-01-11)
+ CMD check, test_that BiocCheck all pass.

Changes in version 0.81.2 (2019-01-11)
+ BiocCheck() compliance increased: 
    o seq functions used instead of :
    o vapply is used instead of sapply.

Changes in version 0.81.1 (2019-01-10)
+ A vignette has been created. 
+ A visual bug, making the colors reversed in the residual plot function 
+ compared to the dWilcox and DSplsda functions has been removed. 
+ Formatting to satisfy the BioConductor criteria has been added.
+ Tests have been adapted to work after reformatting
+ No actual changes have been added to the code. 

Changes in version 0.80.3 (2019-01-09)
+ This is the first time the NEWS file is present. 
+ For all previous changes, and those are hundreds, see the git push messages. 