版本0.99.7(2018-02-14)+最后版本支持hpAnnot作为注释包0.99.8(2018-03-07)+第一个版本使用AnnotationHub加载注释文件。版本0.99.9(2018-03-09)+适应SummarizedExperiment和MultiAssayExperiment hipathia包。版本0.99.27(2018-04-08)+纠正Bionconductor风格版本1.0.1(2018-06-14)+固定小虫在heatmap_plot方差以防variable_cluster = TRUE。+ visualize_report修复轻微缺陷。+添加test_package。R文件。1.1.2版本(2018-09-07)+添加基因的名字在图表工具提示+修复bug。R,保存。R,统计数据。1.3.1 R版本(2018-12-17)+修复bug在get_pathways_summary“薪酬”是有序的。+小增加装饰图案。1.3.2(2019-01-29)+版本修复bug在do_wilcoxon“薪酬”是有序的。 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