CHANGES IN VERSION 2.3.6
------------------------
 o add readable parameter in simplot <2014-10-09, Thu>

CHANGES IN VERSION 2.3.5
------------------------
 o implement enrichMap <2014-07-28, Wed>

CHANGES IN VERSION 2.3.4
------------------------
 o return ggplot2 objects in gseaplot <2014-07-21, Mon>

CHANGES IN VERSION 2.3.3
------------------------
 o geneSim can only accept one gene ID vector and perform as mgeneSim in GOSemSim <2014-06-23, Mon>
 o update man files <2014-06-23, Mon>

CHANGES IN VERSION 2.3.2
------------------------
 o bug fixed in scaleNodeColor <2014-06-08, Sun>

CHANGES IN VERSION 2.3.1
------------------------
 o upgrade man file according to roxygen2 (ver 4.0.0) . <2014-05-16, Fri>

CHANGES IN VERSION 1.99.6
------------------------
 o bug fixed in EXTID2NAME. <2013-09-28, Sat>

CHANGES IN VERSION 1.99.5
------------------------
 o fixed in calculating M when only one categroy presented, the object was matrix insted of list. <2013-09-16, Mon>

CHANGES IN VERSION 1.99.4
------------------------
 o export gsea function <2013-07-10, Wed>

CHANGES IN VERSION 1.99.3
------------------------
 o extend EXTID2NAME to support 20 species <2013-07-09, Tue>
 o update vignette. <2013-07-09, Tue>

CHANGES IN VERSION 1.99.1
------------------------
 o convert vignette file to knitr Sweave. <2013-06-24, Mon>

CHANGES IN VERSION 1.99.0
------------------------
 o extent ggplot to support enrichResult by implementing fortify method. <2013-05-22, Wed>
 o re-implement barplot.enrichResult. <2013-05-23, Thu>
 o enrich.internal support user specifiy background by parameter universe. <2013-05-24, Fri>
 o implement Gene Set Enrichment Analysis algorithm. <2013-05-29, Wed>
 o change setReadable to support groupGO of clusterProfiler. <2013-05-29, Wed>
 o fixed mclapply not support Windows platform issue. <2013-05-30, Fri>
 o rename logFC parameter to foldChange. <2013-06-13, Thu>

CHANGES IN VERSION 1.7.1
------------------------
 o use geom_bar(stat="identity") instead of geom_bar() in barplot for explicitly mapping y value. <2013-05-08, Wed>
 o bug fixed when qvalue can't calculated. <2013-05-02, Thu>
 o bug fixed of enrich.internal, drop those genes that without annotation when calculating sample gene number. <2013-05-02, Thu>
 o change some code to satisfy ReactomePA <2013-03-27, Wed>

CHANGES IN VERSION 1.5.1
------------------------
 o bug fixed in enrich.internal, now return NA rather than throw error, if gene have no ontology annotation <2013-01-22, Fri>

CHANGES IN VERSION 1.3.2
------------------------
 o update codes of plot functions accompaning with ggplot2 (version 0.9.2) <2012-09-06, Thu>
 o update cnetplot corresponding to igraph version 0.6 <2012-07-11, Wed>
 o parameter showCategory now support term ID vector <2012-07-11, Wed>
 o import termSim and combineScores from GOSemSim. <2012-06,14, Thu>
 o optimize setReadable <2012-05-09, Wed>
 o bug fixed of setReadable method. For those unmapped genes, return the original gene ID. <2012-05-15, Tue>
 o fill color in barplot for Ontology classification. <2012-05-22, Tue>
 o update color scale of cnetplot <2012-06-18, Mon>

CHANGES IN VERSION 1.3.1
------------------------
 o update color scheme of cnetplot <2012-04-10, Tue>
 o add simplot for plotting semantic similarity matrix <2012-04-20, Fri>
 o bug fixed of combineScore function for DO semantic similarity matrix
   which containing NA rows of NA coloumns <2012-04-20, Fri>
 o export doSim and geneSim functions <2012-04-20, Fri>

CHANGES IN VERSION 1.1.12
------------------------
 o implement barplot for enrichResult <2012-03-18, Sun>
 o bug fixed for setReadable method <2012-03-19, Mon>
 o add logFC parameter for cnet plot, support color gene nodes by
   their expression value (log fold change) <2012-03-21, Wed>
 o add mapping entrezgene ID and gene Name for organisms
   other than human, mouse and yeast. <2012-03-22, Thu>
 o bug fixed for attempt to name logFC, when it is NULL. <2012-03-22, Thu>
 o optimized readable method. <2012-03-26, Mon>

CHANGES IN VERSION 1.1.11
------------------------
 o setReadable method for mapping gene ID to gene Symbol in enrichResult instance. <2012-03-12, Mon>
 o export method show. <2012-03-12, Mon>

CHANGES IN VERSION 1.1.10
------------------------
 o import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat>
 o Add DO2ALLEG and EG2ALLDO, for mapping undirecte annotation. <2012-03-03, Sat>
 o update vignette <2012-03-06, Tue>

CHANGES IN VERSION 1.1.9
------------------------
 o fixed BibTeX database file .bib.
   month = , must be month = someMonth, or totally deleted,
   leave it blank will cause texi2dvi failed. <2012-03-01, Thu>
 o update IC data and DO-EG mapping data. <2012-03-01, Thu>

CHANGES IN VERSION 1.1.8
------------------------
 o update vignette, add semantic similarity algorithms' details. <2012-02-28, Tue>

CHANGES IN VERSION 1.1.7
------------------------
 o fixed warnings concerning documents of plot generics. <2012-02-27, Mon>
 o import summary generic from BiocGenerics instead of stats4. <2012-02-27, Mon>

CHANGES IN VERSION 1.1.6
------------------------
 o defined S3 generic for ALLEXTID, EXTID2NAME, EXTID2TERMID, TERM2NAME,
   and TERMID2EXTID. <2012-02-26, Sun>
 o update roxygen and regenerate man file. <2012-02-26, Sun>
 o import S4 generics of plot from BiocGenerics.  <2012-02-26, Sun>

CHANGES IN VERSION 1.1.5
------------------------
 o add S4 method of plot, which accept parameter type = "cnet",
   and call cnetplot.enrichResult method. <2012-02-23, Thu>
 o add S3 method cnetplot.enrichResult for plotting enrichResult object.
   <2012-02-23, Thu>
 o define cnetplot function for category-gene network visualization. <2012-02-23, Thu>
 o remove generic definition of show and summary,
   import show from methods and summary from stats4 <2012-02-23, Thu>
 o redefine functions as S3 methods for mapping ID among gene and Term.
   this will make enrich.internal which calling these mapping function more robust
   <2012-02-23, Thu>

CHANGES IN VERSION 1.1.4
------------------------
 o add Enrichment Analysis session in vignette. <2012-02-22, Wed>
 o optimize enrichDO, ten time faster. <2012-02-22, Wed>
 o separate code of enrichDO to enrich.internal, make it more general,
   and can be applied to other ontology. <2012-02-22, Wed>
 o rename enrichDOResult class to enrichResult and add slot geneInCategory. <2012-02-22, Wed>
 o export infoContentMethod and wangMethod. <2012-02-22, Wed>

CHANGES IN VERSION 1.1.3
------------------------
 o update infoContentMethod to make it consistent between DOSE and GOSemSim. <2011-12-31, Sat>

CHANGES IN VERSION 1.1.2
------------------------
 o change to using roxygen for generating Rd docs

CHANGES IN VERSION 1.1.1
------------------------
 o add function rebuildAnnoData
 o update Disease-Gene Mapping data

CHANGES IN VERSION 0.99.7
------------------------
 o fixed bug in .SemVal_internal

CHANGES IN VERSION 0.99.6
------------------------
 o Use qvalue instead of fdrtool to calculate qvalues.

