Changes in version 4.5.1                        

    o   Convert log(P-values) back to P-values for human using a chi-sq distribution
	Version 4:

    o   New algorithm for human backgrounds

    o   New function: toPWM() that takes both PFMs and PPMs

                         Changes in version 3.5                         

    o   After further testing revert back to PWMEnrich 2.x group P-value algorithm

    o   Introduced group sorting by top motifs

                        Changes in version 3.1.4                        

    o   New way of estimating P-value for groups of sequences. Note this will produce different P-values for groups of sequences than PWMEnrich 2.x !

                        Changes in version 2.4.4                        

    o   Vignette update and fix naming of columns in the motif enrichment report

                        Changes in version 2.4.2                        

    o   Improve promoter selection for human and mouse genomes (duplicates are now disregarded)    

                        Changes in version 2.4.0                        

    o   Major update with more functions and small bugfixes

    o   Added sequenceReport() and groupReport() for easier report generation

    o   Visualise motif scores along a sequence with plotMotifScores()

    o   Creation of empirical CDFs for motif scores

    o   Almost complete rewrite of the vignette to emphasize the main use cases

    o   Converted documenation to roxygen2

                        Changes in version 2.3.2                        

    o   Subsetting functions for backgrounds from Diego Diez

                        Changes in version 2.3.1                        

    o   Fix a bug with plotTopMotifsSequence() with calling an unknown function 

    o   Implement group.only for all background, not only pval in motifEnrichment()

    o   New default to plotMultipleMotifs() so the margins are better

                         Changes in version 2.2                         

    o   Bioconductor 2.12 release version (same as 2.0.0)    

                        Changes in version 2.0.0                        

    o   General cleanup of the code with various small optimisations

    o   A FASTA file name is now also taken as input to motifEnrichment()

    o   The output of motifEnrichment() is now wrapped into a class MotifEnrichmentResults
	that provides a number of convenience methods for common tasks like ranking and
	plotting motifs

    o   Functions makeBackground() and getBackgroundFrequencies() can now take BSgenome 
	objects as input. Thanks to Diego Diez for suggesting this and providing the code. 

    o   Another version of motifScores() has been implemented that requires large amounts
	of memory, but is at least 2 times faster than the old motifScores() implementation.
	Use a new option useBigMemoryPWMEnrich() to switch to this implementation.   

    o   PFMtoPWM now accepts a new parameter seq.count so that MotifDb motifs that are 
	expressed as probabilities instead of frequencies can be easily used.  

                        Changes in version 1.3.0                        

    o   Bioconductor 2.11 release version    

                        Changes in version 1.0.2                        

    o   Use core package parallel instead of doMC

                        Changes in version 1.0.1                        

    o   Fix a typo in test cases and remove doMC as build dependency

                        Changes in version 1.0.0                        

    o   Initial release of the package