Changes in version 1.17.4 (2023-08-14)
+ Adding collapse package to the description file.
+ Correction of the generateSparseData function.
+ Set.seed removed from two places and now non-present in the package.

Changes in version 1.17.3 (2023-07-26)
+ Correction to groupProbPlot, as the last version threw out the most significant
    cells.

Changes in version 1.17.2 (2023-07-14)
+ Correction to scale in groupProbPlot.

Changes in version 1.17.1 (2023-07-13)
+ A mode option is added to the neighSmooth function.
+ The scale of the groupProbPlot output is corrected, to -100, over 50 to 100.

Changes in version 1.11.4/5 (2022-03-17/27)
+ sPLSDA function testing excluded from BioConductor, as it works locally, but
    fails at BioConductor.

Changes in version 1.11.3 (2022-03-12)
+ Bug fix in dColorPlot affecting character vectors and factors used as input.

Changes in version 1.11.2 (2022-03-11)
+ Searching for unidentified bug in test for dSlsda function.

Changes in version 1.11.1 (2022-03-05)
+ Bug fix in dColorPlot, solving problems with individual continuous vectors
+ microClust, an internal function, has been updated to include the counting of
    donors in addition to median and mean calculations among the neighbors.
+ The addition of nUniqueNeihgDons, in conjunction to the aforementioned change
    to the microClust function.
+ Minor updates to dSplsda function testing, to hopefully remove the problem of
    intermittent problems in the testing on the Linux plaform.

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.
