CHANGES IN VERSION 2.6.3 ------------------------ o Switching from edgeR's likelihood ratio test to the preferred quasi-likelihood approach as outlined in the F1000 paper https://f1000research.com/articles/5-1438/v2 o heatmap features: row scaling, fixed group colors, log-transformation o flat file download from html tables CHANGES IN VERSION 2.4.1 ------------------------ o Adding a min.cpm filter for RNA-seq data to de.ana CHANGES IN VERSION 2.3.2 ------------------------ o Additional sbea methods: gsa, mgsa, padog, globaltest, roast, camera, gsva o Additional nbea methods: netgsa, degraph, topologygsa, ganpa, cepa CHANGES IN VERSION 2.1.15 ------------------------- o Slight modification on ORA's hypergeometric p-value calculation according to http://mengnote.blogspot.de/2012/12/calculate-correct-hypergeometric-p.html CHANGES IN VERSION 2.1.14 ------------------------- o Adapting GGEA to also deal with 2-column GRNs CHANGES IN VERSION 2.1.12 ------------------------- o Adapting SPIA to deal with non-kegg gene sets CHANGES IN VERSION 2.1.10 ------------------------- o Including EmpiricalBrownsMethod (ebm) among sbea methods CHANGES IN VERSION 1.99.6 ------------------------- o adaption of specific local statistics for RNA-seq data for sample-permutation methods GSEA, SAFE, and SAMGS CHANGES IN VERSION 1.99.5 ------------------------- o Including PathNet among nbea methods CHANGES IN VERSION 1.99.3 ------------------------- o GSEA permutation approximation based on npGSEA o extended combination functionality CHANGES IN VERSION 1.99.1 ------------------------- o major overhaul of the look'n'feel based on ReportingTools o interactive graphics using imageMap o reworked set and graph view o new kegg view based on pathview CHANGES IN VERSION 1.1.3 ------------------------ o de.ana: extensions for RNA-seq now includes DESeq and edgeR o get.go.genesets: new getter for GO genesets CHANGES IN VERSION 1.1.1 ------------------------ o de.ana: now based on limma functionality o ggea.graph: extended control of layout o ggea: * permutation p-value now based on fast edge resampling * p-value approximation now based on gaussian mixture * extended control for edge selection (consistency threshold, edge type, ...) CHANGES IN VERSION 1.0.0 ------------------------ o EnrichmentBrowser 1.0.0: Initial release of the 'EnrichmentBrowser' package