CHANGES IN VERSION 1.19.1
------------------------
 o update startup message <2016-11-09, Wed>

CHANGES IN VERSION 1.18.0
------------------------
 o BioC 3.4 released <2016-10-18, Tue>

CHANGES IN VERSION 1.17.4
------------------------
 o unit test <2016-08-15, Mon>

CHANGES IN VERSION 1.17.3
------------------------
 o move getDb from GOSemSim (no longer need this function) to ReactomePA and remove dependency of GOSemSim <2016-07-06, Wed>
 o 'by' parameter for GSEA analysis <2016-07-04, Mon>

CHANGES IN VERSION 1.17.2
------------------------
 o use byte compiler <2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/ReactomePA/commit/6ce32c8e03e1b252662a07901cce022fab038086

CHANGES IN VERSION 1.17.1
------------------------
 o https://github.com/Bioconductor-mirror/ReactomePA/commit/5d150f5fe545cfa3983872bf5485af1b9ba3129d

CHANGES IN VERSION 1.16.0
------------------------
 o BioC 3.3 released <2016-05-05, Thu>

CHANGES IN VERSION 1.15.6
------------------------
 o fixed issue of duplicated name in PATHID2NAME <2016-04-21, Thu>

CHANGES IN VERSION 1.15.5
------------------------
 o add maxGSSize parameter <2016-03-10, Thu>
 o update ReactomePA citation info <2016-02-17, Wed>

CHANGES IN VERSION 1.15.4
------------------------
 o according to the update of DOSE <2015-12-20, Sun>

CHANGES IN VERSION 1.15.3
------------------------
 o update citation info <2015-11-24, Tue>

CHANGES IN VERSION 1.15.2
------------------------
 o update vignette <2015-11-16, Mon>

CHANGES IN VERSION 1.15.1
------------------------
 o update vignette <2015-10-28, Wed>

CHANGES IN VERSION 1.14.0
------------------------
 o BioC 3.2 Branch

CHANGES IN VERSION 1.13.5
------------------------
 o add support of fly (Drosophila melanogaster) <2015-09-22, Tue>

CHANGES IN VERSION 1.13.4
------------------------
 o update vignette <2015-08-19, Wed>

CHANGES IN VERSION 1.13.3
------------------------
 o add citation of ChIPseeker <2015-07-09, Thu>
 o add 'Pathway analysis of NGS data' section in vignette <2015-06-29, Mon>
 o convert vignette from Rnw to Rmd <2015-06-29, Mon>

CHANGES IN VERSION 1.13.2
------------------------
 o enable other organisms for viewPathway by Vladislav Petyuk <2015-05-28, Thu>
   see https://github.com/GuangchuangYu/ReactomePA/pull/1

CHANGES IN VERSION 1.13.1
------------------------
 o update enrichMap and viewPathway <2015-05-13, Wed>

CHANGES IN VERSION 1.11.9
------------------------
 o use mapIds instead of mget in TERM2NAME. mapIds will not throw error when pathID is old/deprecated. <2015-04-10, Fri>

CHANGES IN VERSION 1.11.8
------------------------
 o according to https://support.bioconductor.org/p/63024/#66438, modify gsePathway to only test pathways. <2015-04-09, Thu>

CHANGES IN VERSION 1.11.7
------------------------
 o update use_internal_data parameter to ... according to the change of DOSE <2015-04-01, Wed>

CHANGES IN VERSION 1.11.6
------------------------
 o update according to DOSE <2015-03-31, Tue>
   add use_internal_data parameter in internal functional of enrichPathway.

CHANGES IN VERSION 1.11.5
------------------------
 o update according to DOSE <2015-03-01, Sun>
   add use_internal_data parameter in getGeneSet.

CHANGES IN VERSION 1.11.2
------------------------
 o remove import org.Hs.eg.db <2015-01-22, Thu>

CHANGES IN VERSION 1.11.1
------------------------
 o fix some pathways don't have a name <2014-11-17, Mon>
    ## > get("5493857", reactomePATHID2EXTID)
    ##  [1] "510850" "523328" "282187" "282188" ...
    ## > get("5493857", reactomePATHID2NAME)
    ## Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
    ##   value for "5493857" not found

--> This is not a bug in ReactomePA, but an issue of reactome.db, refer to:
--> https://support.bioconductor.org/p/63024/


CHANGES IN VERSION 1.9.4
------------------------
 o add gseaplot function <2014-07-31, Thu>

CHANGES IN VERSION 1.9.3
------------------------
 o import enrichMap from DOSE <2014-07-31, Thu>

CHANGES IN VERSION 1.9.2
------------------------
 o update roxygen to version 4 <2014-06-09, Mon>

CHANGES IN VERSION 1.9.1
------------------------
 o bug fixed of TERM2NAME.Reactome <2014-04-21, Mon>

CHANGES IN VERSION 1.7.2
------------------------
 o bug fixed for multi-organisms support <2013-12-09, Mon>

CHANGES IN VERSION 1.5.3
------------------------
 o bug fixed in TERMID2EXTID <2013-09-18, Wed>

CHANGES IN VERSION 1.5.2
------------------------
 o implement gseAnalyzer for GSEA analysis <2013-07-10, Wed>
 o implement viewPathway for visualizing pathway <2013-07-10, Wed>

CHANGES IN VERSION 1.5.1
------------------------
 o extend enrichPathway to support rat, mouse, celegans, zebrafish, and fly. <2013-03-27, Wed>
 o modify enrichPathway according to the change of enrich.internal, remove qvalueCutoff parameter,
   add pAdjustMethod, add universe paramter for user to specify background. <2013-05-29, Wed>

CHANGES IN VERSION 1.3.1
------------------------
 o bug fixed of ALLEXTID. <2013-03-1, Fri>

CHANGES IN VERSION 1.1.1
------------------------
 o remove geneID2Name, instead import EXTID2NAME from DOSE. <2012-03-12, Mon>
 o remove most of the codes in enrichPathway, instead import enrich.internal in DOSE.
   implement some S3 method for mapping.
   pathID2Name was rename to TERM2NAME, which will called by enrich.internal. <2012-03-12, Tue>

CHANGES IN VERSION 0.99.0
------------------------
 o change package name to ReactomePA, for there is already an RPA package. <2012-03-02, Fri>
 o Vignette issues:  <2012-03-02, Fri>
   	    change image format from .eps to .pdf, make it easier to build.
	    remove the tolatex tag of sessionInfo(), make the output more readble.
 o re-implement geneID2Name using select method. <2012-03-02, Fri>
 o add examples in man pages. <2012-03-02, Fri>
 o remove man pages of internal functions. <2012-03-02, Fri>
 o import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat>
 o add Methods section in enrichPathwayResult-class man page. <2012-03-05, Mon>

CHANGES IN VERSION 0.2.3
------------------------
 o @exportMethod plot <2012-02-15 Wed>
 o fix bug when calling summary method from plot,
   for summary defined in base is S3 method,
   instead import summary generic from stats4 <2012-02-15 Wed>

CHANGES IN VERSION 0.2.2
------------------------
 o remove generic definition of show, summary and plot, add NAMESPACE import show
   from methods and plot from graphics. summary need not to import, for is defined
   in the base package  <2012-02-10 Fri>

CHANGES IN VERSION 0.2.1
------------------------
 o update vignette <2012-02-09 Thu>
 o add sample data (an example list of genes from ProfCom:
   http://webclu.bio.wzw.tum.de/profcom/gene_Lists/example1.txt
   the gene symbols were converted to entrezgene) <2012-02-09 Thu>

CHANGES IN VERSION 0.2.0
------------------------
 o separate codes of mapping pathway ID to pathway Name to a new function pathID2Name <2012-02-09 Thu>
 o implement geneID2Name function for mapping gene ID to gene Symbol <2012-02-09 Thu>
 o add parameter readable in function enrichPathway <2012-02-09 Thu>
 o implement cnetplot for plotting category net <2012-02-09 Thu>
 o modify plot function for class enrichPathwayResult to use cnetplot <2012-02-09 Thu>

CHANGES IN VERSION 0.1.1
------------------------
 o add vignette <2012-02-08 Wed>
 o bug fixed for multiple mapping of pathway ID to pathway Name
   such as pathway 162906 can mapping to 1629061
   and 1629062 when getting pathway name, remain the first one. <2012-02-08 Wed>

CHANGES IN VERSION 0.1.0
------------------------
 o implement show, summary and plot method for enrichPathwayResult class <2012-02-08 Wed>
 o define class enrichPathwayResult to store result of enrichPathway <2012-02-08 Wed>
 o implement enrichPathway function for enrichment analysis.
   using hypergeometric model <2012-02-08 Wed>
 o initial package skeleton <2012-02-08 Wed>


