CHANGES IN VERSION 2.22.0 ------------------------- o GO gene sets: option for hierarchical annotation (new argument `hierarchical` for function `getGenesets`) CHANGES IN VERSION 2.20.0 ------------------------- o New function `import` to import results from differential expression analysis with limma, edgeR, and DESeq2 o New function `showAvailableSpecies` to list supported species for a gene set database of choice (GO, KEGG, MSigDB, Enrichr, ...) o New function `showAvailableCollections` to list provided gene set collections for a supported species of a gene set database of choice (GO, KEGG, MSigDB, Enrichr, ...) o Gene sets: obtaining and caching of gene sets for different gene ID types (new argument `gene.id.types` for function `getGenesets`) o GO gene sets: filter by GO evidence codes (new argument `evid` for function `getGenesets`) o Including NEAT among nbea methods CHANGES IN VERSION 2.18.0 ------------------------- o Gene sets: supporting additional gene set databases - getGenesets(db = "msigdb") to obtain gene sets from the MSigDB for 11 different species (via msigdbr) - getGenesets(db = "enrichr") to obtain gene set libraries from Enrichr for 5 different species o Gene ID mapping for gene sets and gene regulatory networks (function `idMap`) o Implementation of a variance-stabilizing transformation for RNA-seq data (function `normalize` with argument `norm.method = "vst"`) to simplify the application of legacy enrichment methods CHANGES IN VERSION 2.12.0 ------------------------- o Major refactoring of ID mapping for the rownames of a SummarizedExperiment: (functions idMap / probe2gene): - to.ID can also be a rowData column to support user-defined mappings - support of data-driven strategies for many:1 and 1:many mappings - synchronized behavior of microarray probe ID mapping (probe2gene) and general gene ID mapping (idMap) o Alternative representation of gene sets based on GSEABase::GeneSet and GSEABase::GeneSetCollection to facilitate gene ID mapping for gene sets (function getGenesets) o Output destination of HTML reports (functions eaBrowse / ebrowser): extended control via arguments out.dir and report.name that overwrite corresponding config defaults (configEBrowser) o Separation of nominal and adjusted p-values in DE and EA result tables (functions deAna / sbea / nbea) 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