Changes in version 3.11.2 (2026-03-25)                 

    o   Fist version using Zenodo as repository for necessary files

                 Changes in version 2.99.0 (2022-12-01)                 

    o   Adding parameters uni.terms and GO.terms to hipathia, to compute functional activity within this function.

    o   Adding functions DAcomp, DAtop, DAsummary, DAoverview, define_colors, plotVG, DAreport. 

    o   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

                 Changes in version 2.13.1 (2022-07-27)                 

    o   Fixing bug in nodes DE with limma with high rates of 0-variance genes. 

                 Changes in version 2.3.2 (2019-05-17)                  

    o   Correcting bug in non-public do_limma function: experimental designs with more than two experimental conditions were not well treated.

                 Changes in version 2.1.1 (2019-05-17)                  

    o   Adding function mgi_from_sif, which allows to create a pathways object from SIF + ATT files.

                 Changes in version 1.5.1 (2019-02-21)                  

    o   Adding function node_color

    o   Including parameter adjust in node_color_per_de function. Set TRUE as default, previously considered as FALSE

    o   Allowing node_colors_per_de to accept any experimental design accepted by limma::makeContrasts.

    o   Removing non-visible function compute_difexp

    o   Adding GO IDs to GO annotations and making them the rownames of the go_vals matrix

    o   Adding get_go_names function, to translate GO Ids to GO function names

    o   Adapting to new RData names in AnnotationHub, which include the version of the data in hpAnnot files.

    o   Restricting GO names to 50 characters.

    o   Adding group.by slot to metaginfo objects.

                 Changes in version 1.3.2 (2019-01-29)                  

    o   Fixing bug in do_wilcoxon when "comp" is ordered.

                 Changes in version 1.3.1 (2018-12-17)                  

    o   Fixing bug in get_pathways_summary when "comp" is ordered.

    o   Minor adding to vignette.

                 Changes in version 1.1.2 (2018-09-07)                  

    o   Adding gene name to tooltip

    o   Fixing minor bugs in chart.R, save.R, stats.R

                 Changes in version 1.0.1 (2018-06-14)                  

    o   Fixing minor bug in heatmap_plot about variances in case variable_cluster = TRUE.

    o   Fixing minor bug in visualize_report.

    o   Adding test_package.R file.

                Changes in version 0.99.27 (2018-04-08)                 

    o   Correcting Bionconductor style

                 Changes in version 0.99.9 (2018-03-09)                 

    o   Adapting hipathia package to SummarizedExperiment and MultiAssayExperiment.

                 Changes in version 0.99.8 (2018-03-07)                 

    o   First version using AnnotationHub to load annotation files.

                 Changes in version 0.99.7 (2018-02-14)                 

    o   Last version supporting hpAnnot as annotation package