NEWS

EnrichmentBrowser 2.22.0

GO gene sets: option for hierarchical annotation (new argument 'hierarchical' for function 'getGenesets')

New function 'import' to import results from differential expression analysis with limma, edgeR, and DESeq2
New function 'showAvailableSpecies' to list supported species for a gene set database of choice (GO, KEGG, MSigDB, Enrichr, ...)
New function 'showAvailableCollections' to list provided gene set collections for a supported species of a gene set database of choice (GO, KEGG, MSigDB, Enrichr, ...)
Gene sets: obtaining and caching of gene sets for different gene ID types (new argument 'gene.id.types' for function 'getGenesets')
GO gene sets: filter by GO evidence codes (new argument 'evid' for function 'getGenesets')
Including NEAT among nbea methods

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
Gene ID mapping for gene sets and gene regulatory networks (function 'idMap')
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

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)
Alternative representation of gene sets based on GSEABase::GeneSet and GSEABase::GeneSetCollection to facilitate gene ID mapping for gene sets (function getGenesets)
Output destination of HTML reports (functions eaBrowse / ebrowser): extended control via arguments out.dir and report.name that overwrite corresponding config defaults (configEBrowser)
Separation of nominal and adjusted p-values in DE and EA result tables (functions deAna / sbea / nbea)

Adding scripts to inst/scripts to invoke the EnrichmentBrowser from the command line (for non-R users)
GRN compilation: supporting additional pathway databases (via graphite)
Caching for download of GO and KEGG gene sets (via BiocFileCache)
Default output destination changed to rappdirs::user_data_dir("EnrichmentBrowser")
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

Slight modification on ORA's hypergeometric p-value calculation according to http://mengnote.blogspot.de/2012/12/calculate-correct-hypergeometric-p.html
Adapting GGEA to also deal with 2-column GRNs
Adapting SPIA to deal with non-kegg gene sets
Including EmpiricalBrownsMethod (ebm) among sbea methods

major overhaul of the look'n'feel based on ReportingTools
interactive graphics using imageMap
reworked set and graph view
new kegg view based on pathview
adaption of specific local statistics for RNA-seq data for sample-permutation methods GSEA, SAFE, and SAMGS
Including PathNet among nbea methods
GSEA permutation approximation based on npGSEA
extended combination functionality

de.ana: extensions for RNA-seq now includes DESeq and edgeR
get.go.genesets: new getter for GO genesets
de.ana: now based on limma functionality
ggea.graph: extended control of layout
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, ...)