EGSEA 1.1.1 (2016-05-10)
------------------------
- Improved: topSets(...) and the functionality of the "report" argument in the egsea(...) function.
- Improved: verbosity and "print.base" usability in egsea(). The statistics of individual methods can
now be exported in the output of egsea when print.base = TRUE. 
- Added: the fry(...) gene set test from the limma package.
- Added: multiple methods to combine the p-values of multiple methods. See egsea.combine().
- Fixed: various minor bugs. 

EGSEA 1.1.4 (2016-05-23)
------------------------
- Improved: ORA to adapt a cut-off threshold logFC=0 if no DE genes were 
found at logFC=1. In both cases, the cut-off threshold of adjusted p-value = 0.05.
- Improved: the robustness of the package and allows for single GSE analysis to be
carried out using EGSEA. 
- Added: Ensemble mode is disabled if one base GSE method is provided.
- Added: S4 class for the egsea() output, named EGSEAResults.
- Added: generic methods: show(), summary(), plotHeatmap(), plotPathway(), plotMDS(), 
and plotSummary(). 


EGSEA 1.1.5 (2016-05-27)
------------------------
- Fixed: a minor bug in EGSEAResults when symbolsMap = NULL
- Added: NA Gene Symbols are replaced with Feature IDs in the symbolsMap
- Added: FRY to egsea.base()
- Added: several sanity checks on the input parameters

EGSEA 1.1.6 (2016-05-31)
------------------------
- Fixed: a minor bug in the calculation of the comparative analysis p-value.

EGSEA 1.1.7 (2016-06-30)
------------------------
- Improved: the documentation of the methods in the vignette 
- Improved: the interpretation of the results in the vignette 
- Improved: the ranking when ties occur
- Added: useDingbats = FALSE to pdf() when generating summary plots
- Added: S4 class named GSCollectionIndex to store indexed gene set collections
- Added: showSetByName() and showSetByID() to EGSEAResults and GSCollectionIndex
- Added: plotGOGraph() to EGSEAResults
- Updated: the GO graphs page of the comparative analysis
- Added: GO graphs to the GO collection of the GeneSetDB
- Fixed: minor bugs

EGSEA 1.1.8 (2016-07-12)
------------------------
- Removed: EGSEAResults of IL13 from EGSEA and moved it to EGSEAdata
- Updated: EGSEAdata object names in idxAnno

EGSEA 1.1.9 (2016-08-19)
------------------------
- Fixed: a bug in buildIdx of mouse H gene set 

EGSEA 1.1.10 (2016-)
------------------------
- Added: two slots to the GSCollectionIndex: version and date
- Added: citations of the base methods to the documentation of egsea.base()
- Removed: rdata.dir from buildIdx functions
- Added: the gene set collection version/update date to the GSCollectionIndex class
- Added: an argument to egsea() and egsea.cnt() to return the analysis of limma results, which is
keep.imma 
- Added: an argument to egsea() and egsea.cnt() to return the set scores of ssgsea, keep.set.scores
- Added: a slot to the EGSEAResults, which is limmaResults
- Added: a slot to the EGSEAResults, baseInfo
- Added: limmaTopTable, getlimmaResults and getSetScores to the class EGSEAResults
- Added: plotSummaryHeatmap to the class EGSEAResults 
- Improved: documentation across several functions. 



