CHANGES IN VERSION 1.21.1
-------------------------

BUG FIXES

    o Fixed ENSEMBL host for rnorvegicus_gene_ensembl. Using default host now instead of may2012.archive.ensembl.org.
    
    
CHANGES IN VERSION 1.14.2
-------------------------

BUG FIXES

    o Corrected format check for experiment.table: Spaces are not excepted any longer, because they lead to downstream errors.


CHANGES IN VERSION 1.14.1
-------------------------

BUG FIXES

    o Compatibility update: Replaced class() checks with is().


CHANGES IN VERSION 1.13.1
-------------------------

BUG FIXES

    o Compatibility update: Replaced deprecated fetchExtendedChromInfoFromUCSC() with getChromInfoFromUCSC().


CHANGES IN VERSION 1.11.1
-------------------------

BUGFIXES

    o Bugfix for error when exporting empty peaks in univariateHMM.
    
    
CHANGES IN VERSION 1.9.2
------------------------

BUGFIXES

    o Bugfix for error when exporting empty peak lists.


CHANGES IN VERSION 1.7.2
------------------------

BUGFIXES

    o Compatibility fixes for the new release of ggplot2 (3.0.0).
    
    o seqlevels() that are smaller than binsize are dropped properly in fixedWidthBins() and variableWidthBins().
    
    
CHANGES IN VERSION 1.5.3
------------------------

SIGNIFICANT USER-LEVEL CHANGES

    o Function 'changePostCutoff()' works on univariate peak calls without posterior needing to be present.
    
    
CHANGES IN VERSION 1.5.1
------------------------

SIGNIFICANT USER-LEVEL CHANGES

    o New column 'maxPostInPeak' containing the maximum posterior within each peak.

    o Score in exported BED files is calculated as -10*log10(maxPostInPeak).
    
    o 'changeFDR()' was renamed to 'changeMaxPostCutoff()'.
    
    
CHANGES IN VERSION 1.3.1
------------------------

NEW FEATURES

    o New parameter 'stepsize' allows sliding bins. This improves localization of peaks.
    
SIGNIFICANT USER-LEVEL CHANGES

    o New default value for Chromstar(..., stepsize = 1/2 * binsize).
    
    
CHANGES IN VERSION 1.1.4
------------------------

BUG FIXES

    o Fixed a mistake in the calculation of differential scores from version 1.1.2
    

CHANGES IN VERSION 1.1.2
------------------------

NEW FEATURES

    o Proper print() methods for all objects.

BUG FIXES

    o Fixed a bug where chromosomes with a single bin were making problems.


CHANGES IN VERSION 1.1.1
------------------------

NEW FEATURES

    o Selection of peaks can be done with 'changeFDR'.

    o Peak calls are available in each chromstaR-object as list entry '$peaks'.

SIGNIFICANT USER-LEVEL CHANGES

    o 'plotFoldEnrichment' renamed to 'plotEnrichment'.

    o 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates' replaced by 'exportCounts', 'exportPeaks', 'exportCombinations'.

BUG FIXES

    o Proper computation of fold enrichments, with < 1 indicating depletion and > 1 indicating enrichment.

DEPRECATED AND DEFUNCT

    o 'changePostCutoff'.

    o 'plotFoldEnrichment'.

    o 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates'.
