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