Changes in version 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.

                        Changes in version 1.1.0                        

  - GeDi is now on Bioconductor.

                       Changes in version 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.

                       Changes in version 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

                       Changes in version 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

                       Changes in version 0.99.0                        

  - Ready for the submission to Bioconductor!

                       Changes in version 0.90.0                        

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

                        Changes in version 0.1.0                        

  - Officially entering the path of the GeDi!