CHANGES IN VERSION 2.40.0
-------------------------

    o getGenesets now supports MSigDB's new designated mouse collections named
      'MH' (hallmark), 'M1'(genomic position), 'M2' (curated databases), and so on.

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
