CHANGES IN VERSION 1.2.3
------------------------
 o when peak is exactly located at gene end, NA will be generated and throw error when assigning downstream of gene end. 
   This bug has been fixed <2015-02-03, Tue>

CHANGES IN VERSION 1.2.2
------------------------
 o bug fixed in getNearestFeatureIndicesAndDistances when peak in the
   very begining or end of the chromosome <2015-01-30, Fri>

CHANGES IN VERSION 1.1.21
------------------------
 o use data.table instead of data.frame to optimize covplot <2014-10-06, Mon>

CHANGES IN VERSION 1.1.20
------------------------
 o seqlengths in GRanges object is deprecated, now use Seqinfo defined by GenomeInfoDb.
   update annotatePeak to store this information <2014-09-30, Tue>
 o runValue (in S4Vector) for RleList is deprecated, 
   modified runValue(x) to sapply(x, runValue) <2014-09-30, Tue>

CHANGES IN VERSION 1.1.19
------------------------
 o implement csAnno S4 object <2014-09-28, Sun>
 o modify plot function for csAnno instance <2014-09-28, Sun>
 o implement vennpie function <2014-09-28, Sun>

CHANGES IN VERSION 1.1.17
------------------------
 o deprecate plotChrCov to new function covplot <2014-08-18, Mon>
 o add new paramter chrs and xlim to covplot <2014-08-18, Mon>

CHANGES IN VERSION 1.1.16
------------------------
 o optimize plotChrCov, running time reduce drastically <2014-08-15, Fri>

CHANGES IN VERSION 1.1.15
------------------------
 o remove un-mappable peak to prevent fail in peak annotation <2014-08-14, Thu>

CHANGES IN VERSION 1.1.14
------------------------
 o bug fixed in plotDistToTSS <2014-08-14, Thu>

CHANGES IN VERSION 1.1.13
------------------------
 o change TranscriptDb to TxDb according to GenomicFeatures <2014-07-29, Tue>

CHANGES IN VERSION 1.1.12
------------------------
 o bug fixed in plotChrCov <2014-07-21, Mon>

CHANGES IN VERSION 1.1.10
------------------------
 o bug fixed in calculating distances from peak end <2014-06-18, Wed>

CHANGES IN VERSION 1.1.9
------------------------
 o add level parameter to annotatePeak, and set it to "transcript" by default. 
   Now annotatePeak will annotate peaks in transcript level 
   except user specify level = "gene" <2014-06-16, Mon>
 o add addFlankGeneInfo parameter to annotatePeak. 
   If it set to true, all features within the flankDistance will be annotated. <2014-06-16, Mon>

CHANGES IN VERSION 1.1.8
------------------------
 o bug fixed when peak overlap with feature <2014-06-11, Wed>
 o optimize for getting overlap features of peaks <2014-06-11, Wed>
 o update plotAnnoPie, separate the pie and legend to prevent label overlap <2014-06-12, Thu>

CHANGES IN VERSION 1.1.7
------------------------
 o bug fixed in calculating distanceToTSS <2014-06-03, Tue>

CHANGES IN VERSION 1.1.6
------------------------
 o add chainFile parameter in enrichAnnoOverlap and enrichPeakOverlap to support different genome version comparision <2014-06-01, Sun>
 o fixed color bug in peakHeatmap.internal2 and plotAnnoBar <2014-06-02, Mon>
 o update vignettes <2014-06-02, Mon>

CHANGES IN VERSION 1.1.5
------------------------
 o export getPromoters and getTagMatrix <2014-05-31, Sat>
 o rename plotAvgProf to plotAvgProf2 and implement plotAvgProf based on tagMatrix  <2014-05-31, Sat>
 o implement tagHeatmap for visualize heatmap of the tagMatrix or a list of tagMatrix <2014-05-31, Sat>
 o implement shuffle function to generate a random ChIP data based on a real one <2014-05-31, Sat>
 o implement enrichPeakOverlap to calcuate significant of ChIP experiments based on the genome coordinations <2014-05-31, Sat>
 o implement enrichAnnoOverlap to calculate significant of ChIP experiments based on their nearest gene annotation <2014-05-31, Sat>
 o incorporate GEO database for mining significant overlap of ChIP data <2014-05-31, Sat>
   + getGEOspecies summarize the collected data by species
   + getGEOgenomeVersion summarize the colleted data by genome version
   + getGEOInfo extract the information by genome version query
   + downloadGEObedFiles download all bed files of a particular genome version
   + downloadGSMbedFiles download the bed files of the input GSM list.

CHANGES IN VERSION 1.1.4
------------------------
 o in the annotation column of output of annotatePeak function, 
	if Exon/Intron, the output change to 'Transcript_Name/GeneID, Exon no. of total_no.' <2014-05-14, Wed>

CHANGES IN VERSION 1.1.3
------------------------
 o bug fixed when metadata(TranscriptDb) contained NA <2014-04-30, Wed>
 o support ID type of Ensembl in annotatePeak (Entrez was supported) <2014-04-30, Wed> 

CHANGES IN VERSION 1.1.2
------------------------
 o implemented plotChrCov <2014-04-25, Fri>
 o implemented plotAvgProf and peakHeatmap <2014-04-24, Thu>

CHANGES IN VERSION 1.1.1
------------------------
 o output of annotatePeak now contain chromosome length information <2014-04-22, Tue>
 o re-implement plotAnnoPie to use ordinary pie plot instead of pie3D <2014-04-21, Mon>

CHANGES IN VERSION 1.0.0
------------------------
 o initial version with the following functions implemented:
   + annotatePeak
   + overlap
   + plotAnnoBar
   + plotAnnoPie
   + plotDistToTSS
   + readPeakFile
   + vennplot
   + vennplot.peakfile