CHANGES IN VERSION 2.10.0 ------------------------- o Adding scripts to inst/scripts to invoke the EnrichmentBrowser from the command line (for non-R users) o GRN compilation: supporting additional pathway databases (via graphite) o Caching for download of GO and KEGG gene sets (via BiocFileCache) o Default output destination changed to rappdirs::user_data_dir("EnrichmentBrowser") o Function names: deprecation of x.x notation - read.eset -> readSE - probe.2.gene.eset -> probe2gene - de.ana -> deAna - compile.grn.from.kegg -> compileGRN - ggea.graph -> ggeaGraph - make.example.data -> makeExampleData CHANGES IN VERSION 2.8.0 ------------------------ o Major migration from ExpressionSet to SummarizedExperiment CHANGES IN VERSION 2.4.0 ------------------------ o Adding a min.cpm filter for RNA-seq data to de.ana o Additional sbea methods: gsa, mgsa, padog, globaltest, roast, camera, gsva o Additional nbea methods: netgsa, degraph, topologygsa, ganpa, cepa CHANGES IN VERSION 2.2.0 ------------------------- o Slight modification on ORA's hypergeometric p-value calculation according to http://mengnote.blogspot.de/2012/12/calculate-correct-hypergeometric-p.html o Adapting GGEA to also deal with 2-column GRNs o Adapting SPIA to deal with non-kegg gene sets o Including EmpiricalBrownsMethod (ebm) among sbea methods CHANGES IN VERSION 2.0.0 ------------------------- 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 o adaption of specific local statistics for RNA-seq data for sample-permutation methods GSEA, SAFE, and SAMGS o Including PathNet among nbea methods o GSEA permutation approximation based on npGSEA o extended combination functionality CHANGES IN VERSION 1.2.0 ------------------------ o de.ana: extensions for RNA-seq now includes DESeq and edgeR o get.go.genesets: new getter for GO genesets 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 Initial release of the 'EnrichmentBrowser' package