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 (2016-08-30)
------------------------
- 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.limma 
- 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. 


EGSEA 1.3.1 (2017-01-28)
------------------------
- Fixed: bug in the row names of limmaTopTable. Thanks to Ali Jalali from MD Anderson for reporting it.
- Fixed: bug in plotSummaryHeatmap when there is only one single contrast. 
- Added: "avg.logFC.Dir" to the EGSEA scores
- Improved: the plotSummaryHeatmap function to work with Direction scores
- Modified: EGSEA scores to be all small letters and updated egsea.sort() accordingly
- Added: median to combining p-values
- Added: plotBars function
- Fixed: bug in buildMSigDBIdx when no genes mapped to c5
- Improved: the wrapper I/O interfaces to become standard
- Improved: the implementation of GSVA by parallelizing the calculations on gene sets and calculating the gene set scores using the whole expression matrix
- Improved: the parallelization of several wrappers 
- Added: ability to accept a design matrix with an intercept and a contrast vector of coefficient indexes. 
- Added: a function to optimize the number of cores to be used for running EGSEA. It helps to avoid CPU overloading. 
- Added: an information about the runnign time of the analysis. 
- Added: a new way of report generation that completely depends on the EGSEAResults object. This allows users to re-generate their reports with different parameter values, e.g., display.top, sort.by, sum.plot.axis, sum.plot.cutoff. 
- Added: summary heatmaps and bar plots to the report. 
- Improved: the colour scheme of the summary heatmaps and bar plots.  
- Fixed: bug in visualizations when log10(x) = Inf
- Added: fdr.cutoff to the calculation of Significance Score and Regulation Direction. 
- Improved: the colour of summary heatmaps. 
- Modified: buildMSigDBIdx to work with C5 collection of version 5.2 

EGSEA 1.3.2 (2017-03-16)
------------------------
- Added: features to allow partitioning GO collections into GO domains