CHANGES IN VERSION 1.4.1
------------------------
 o minor bug fixed in getChrCov <2015-04-27, Mon>
 
CHANGES IN VERSION 1.3.15
------------------------
 o update vignette <2015-03-31, Tue>

CHANGES IN VERSION 1.3.14
------------------------
 o add pool parameter in enrichPeakOverlap <2015-03-30, Mon>
 
CHANGES IN VERSION 1.3.13
------------------------
 o update enrichPeakOverlap to support nShuffle = 0, which now will report only overlay with pvalue = NA <2015-03-29, Sun>
 o add facet and free_y parameter for plotAvgProf and plotAvgProf2 <2015-03-29, Sun>
 o update docs <2015-03-29, Sun>
 o update plotAvgProf and plotAvgProf2 to fully supporting confidence interval,
   see https://github.com/GuangchuangYu/ChIPseeker/pull/6 <2015-03-29, Sun>
 
CHANGES IN VERSION 1.3.12
------------------------
 o add confidence interval for plotAvgProf, see https://github.com/GuangchuangYu/ChIPseeker/issues/3 <2015-03-26, Thu>
 
CHANGES IN VERSION 1.3.11
------------------------
 o add citation <2015-03-16, Mon>
 
CHANGES IN VERSION 1.3.10
------------------------
 o update GEO data <2015-03-03, Tue>
 
CHANGES IN VERSION 1.3.9
------------------------
 o add parameter *genomicAnnotationPriority* for annotatePeak function <2015-02-27, Fri>

CHANGES IN VERSION 1.3.8
------------------------
 o add DOSE citation <2015-02-13, Fri>
 
CHANGES IN VERSION 1.3.7
------------------------
 o bug fixed in plotDistToTSS <2015-02-06, Fri>
 
CHANGES IN VERSION 1.3.6
------------------------
 o when peak is exactly located at gene end and near the end of chromosome,
   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 1.3.5
------------------------
 o bug fixed in getNearestFeatureIndicesAndDistances when peak in the
   very begining or end of the chromosome <2015-01-30, Fri>
 
CHANGES IN VERSION 1.3.4
------------------------
 o bug fixed for introducing dplyr in plotDistToTSS <2015-01-28, Wed>

CHANGES IN VERSION 1.3.3
------------------------
 o update vignette to use BiocStyle::latex() <2015-01-26, Mon>
 
CHANGES IN VERSION 1.3.2
------------------------
 o fixed import issue to meet the changes of AnnotationDbi and S4Vectors <2015-01-22, Thu>

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 update annotatePeak to store the seqinfo information <2014-09-30, Tue>
 o 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
