NEWS

GeDi 1.2.0

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.
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 genesets 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.

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

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

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