# GeDi 1.5.1

* `getJaccardMatrix()`, `getKappaMatrix()`, `getMeetMinMatrix()` and `getSorensenDiceMatrix()`
received a notable speedup in their implementation, thanks to the underlying code now 
based on the sparse matrix operations implemented in the `proxyC` package.
Accordingly, the element-wise functions `calculateJaccard()`, `calculateKappa()`, 
and `calculateSorensenDice()` were removed from this package.
* The Markov clustering function is now relying on an internal function, reducing the
dependency load coming from the `GeneTonic` package. Similarly, `.map_to_color` 
handles the mapping of the values to the colors used in the interactive graph views provided
by `visNetwork`
* `enrichmentWordcloud()` has now the option to filter some generic terms, often 
encountered in the GO terms collection, as they could risk becoming not too 
informative of the underlying processes ( via the `remove_generic_terms` parameter).
Moreover, any custom term can be removed if specified by the `terms_to_remove`
parameter.
* `goDistance()` now uses the efficient implementation of the distances provided 
by the `simona` package, instead of the fairly cumbersome approach taken by `GOSemSim`
* `distanceHeatmap()` has now some additional parameter to fine tune the visual 
looks of the geneset distance heatmap. The `display_similarity` parameter can be
set to TRUE to display the similarity values, instead of the distances, Moreover,
the `quantile_limits` (defaulting to `c(0.025, 0.975)`, the 2.5% and the 97.5% 
quantiles) specifies the thresholds that can be used to winsorize the underlying 
values - extreme values could lead to a wide usage of most of the color palette,
making patterns harder to discern. This behavior can be deactivated by setting the
quantiles to `c(0, 1)`, which would then include the set of values as-is.
* The graph of genesets now includes the calculation of some network based 
statistics, to assist users in the prioritization of which genesets to focus on 
(e.g. after extracting the communities).
* GeDi now implements a new funciton called `path_to_GeDi()`, which can be used 
to transform the output of various enrichment analysis R packages to be directly
usable in `GeDi`. The option include packages such as `topGO`, `clusterProfiler`, 
`ReactomePA`, `enrichR` and `fgsea`.


# GeDi 1.2.0

* Smaller bug and typo fixes

* Fixed the bug that the `getGenes()` function would set all gene names to all 
  caps which lead to the inability to download the correct PPI information for 
  species like mouse. Also renamed the function to `prepareGenesetData()` to 
  reflect more accurately its behavior. 
  
* Updated the default version used in the `getId()` and `getStringDB()` to 12.0, 
  the current version of the String database.
  
* Fixed the broken zoom feature in the Optional Filtering Step in the Data Input
  panel. Additionally added a column Description to the table of zoomed gene sets
  to facilitate interpretation.
  
* Fixed that the clustering will now be reset whenever a new score is calculated.

* Updated the `checkInclusion()` function to drastically reduce runtime.

* Fixed the error that the value of `alpha` would not be properly pass to all the
  sub function used by the `getpMMMatrix()` function.
  
* Replaced all occurrences of PMM with pMM to match the notation of the original
  publication. 
  
* Replaced the kNN clustering algorithm with PAM (partitioning around mendoids) 
  as this seems to be more suitable for enrichment data represented by distance
  scores. 
  
* Renamed the `goSimilarity()` function to `goDistance()` to better indicated 
  that this is a distance rather than a similarity score. Also scaled all 
  scores to the [0, 1] interval.

* Fixed the normalization function in the `getKappaDistanceMatrix()` function.

* Changed the implementation of the Louvain clustering algorithm to use a 
  weighted graph now. The graph is weighted by the distance scores between 
  gene sets.
  
* Added `GeneTonicList` as a possible input object for GeDi. Now GeDi is directly
  compatible with `GeneTonic`.

# GeDi 1.1.0

* GeDi is now on Bioconductor.

# GeDi 0.99.5

* This version reflects further changes performed upon the Bioconductor reviewing process.
* Removed icons from the vignette to reduce the overall size of the package. 

# GeDi 0.99.4

* This version reflects the changes performed upon the Bioconductor reviewing process
* Added `col_name_genesets` and `col_name_genes` as parameter to the `GeDi()` main app to allow users to specify the relevant column names upon executing the command
* Changes in the R code to comply to best practices (replacing single `|` with `||` and similar)
* Loading the example file does not require anymore the setting of `globalVariables()`
* All files retrieved do use some form of caching for avoiding unnecessary re-download operations
* Reworked the allocation of vectors before `for` loops to avoid unhealthy growing of vectors/matrices

# GeDi 0.99.1

* The handling of the parallelization for the distance calculations is now unified
under the umbrella of BiocParallal, and defaults now to using `SerialParam()` to
avoid unexpected behaviors

# GeDi 0.99.0

* Ready for the submission to Bioconductor!

# GeDi 0.90.0

* Final touches and bug fixes to the main functionality
* Deployment of the package website via pkgdown

# GeDi 0.1.0

* Officially entering the path of the GeDi!


