Version 0.99.7 (2018-02-14)
  + Last version supporting hpAnnot as annotation package

Version 0.99.8 (2018-03-07)
  + First version using AnnotationHub to load annotation files.

Version 0.99.9 (2018-03-09)
  + Adapting hipathia package to SummarizedExperiment and MultiAssayExperiment.

Version 0.99.27 (2018-04-08)
  + Correcting Bionconductor style

Version 1.0.1 (2018-06-14)
  + Fixing minor bug in heatmap_plot about variances in case variable_cluster = TRUE.
  + Fixing minor bug in visualize_report.
  + Adding test_package.R file.

Version 1.1.2 (2018-09-07)
  + Adding gene name to tooltip
  + Fixing minor bugs in chart.R, save.R, stats.R

Version 1.3.1 (2018-12-17)
  + Fixing bug in get_pathways_summary when "comp" is ordered.
  + Minor adding to vignette.

Version 1.3.2 (2019-01-29)
  + Fixing bug in do_wilcoxon when "comp" is ordered.

Version 1.5.1 (2019-02-21)
  + Adding function node_color
  + Including parameter adjust in node_color_per_de function. Set TRUE as default, previously considered as FALSE
  + Allowing node_colors_per_de to accept any experimental design accepted by limma::makeContrasts.
  + Removing non-visible function compute_difexp
  + Adding GO IDs to GO annotations and making them the rownames of the go_vals matrix
  + Adding get_go_names function, to translate GO Ids to GO function names
  + Adapting to new RData names in AnnotationHub, which include the version of the data in hpAnnot files.
  + Restricting GO names to 50 characters.
  + Adding group.by slot to metaginfo objects.

Version 2.1.1 (2019-05-17)
  + Adding function mgi_from_sif, which allows to create a pathways object from SIF + ATT files.

Version 2.3.2 (2019-05-17)
  + Correcting bug in non-public do_limma function: experimental designs with more than two experimental conditions were not well treated.

Version 2.13.1 (2022-07-27)
  + Fixing bug in nodes DE with limma with high rates of 0-variance genes. 

Version 2.99.0 (2022-12-01)
  + Adding parameters uni.terms and GO.terms to hipathia, to compute functional activity within this function.
  + Adding functions DAcomp, DAtop, DAsummary, DAoverview, define_colors, plotVG, DAreport. 
  + Modifyng structure of objects, by creating object DAdata, which includes more information than traditional hipathia results object. This includes:
    - Activity values of nodes, paths, and selected functions
    - Extra information about the paths, nodes and functions in rowData elements of the SummarizedExperiments

Version 3.0.1 (2023-06-01)
  + Modifyng vignette to include new pipeline from version 2.99.0
  + Changing verbose style: now the pathway names are never shown, and verbose == TRUE indicates the general steps of the function.
  + Adding custom.terms parameter to function hipathia(), to add a custom functional annotation to be passed to quantify_terms() as parameter dbannot.

Version 3.0.2 (2023-06-05)
  + Fixing bug in vignette caused by warnings in hipathia() function

