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NEWS
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NEWS
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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