Changes in version 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. 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!