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NEWS
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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