CHANGES IN VERSION 1.11.01 (15 April 2018)
--------------------------------------------
+ rm gamma = 1.5 argument for grDevices::rainbow function

CHANGES IN VERSION 1.7.04 (17 April 2017)
--------------------------------------------
get Manual from Bioconductor.org
browseURL('http://www.bioconductor.org/packages/3.4/bioc/vignettes/canceR/inst/doc/canceR.pdf')

CHANGES IN VERSION 1.7.3 (17 February 2017)
--------------------------------------------
dontrun examples

CHANGES IN VERSION 1.7.2 (17 January 2017)
--------------------------------------------
resolve issue when computing mutation frequency

CHANGES IN VERSION 1.5.2 (01 Septembre 2016)
--------------------------------------------
resolve issue 1 about "tl not found"
delete file R/getGeneticProfiles.R
resolve 'no visible binding for global variable'
add R/aaa.R

CHANGES IN VERSION 1.3.91 (01 May 2016)
---------------------------------------
rm canceR.pdf and lines from canceR.Rnw
%\VignetteEngine{R.rsp::tex}
%\VignetteKeyword{R}
%\VignetteKeyword{package}
%\VignetteKeyword{vignette}
%\VignetteKeyword{LaTeX}
%\VignetteAuthor{Karim Mezhoud}
%\VignetteDepends{}
%\VignetteKeywords{A Graphical User Interface for accessing and modeling the MSKCC Cancer Genomics Data.}
%\VignettePackage{canceR}

CHANGES IN VERSION 1.3.7 (07 April 2016)
------------------------
add /extdata/canceR.pdf

CHANGES IN VERSION 1.3.6 (05 April 2016)
------------------------
fix paths in running examples

CHANGES IN VERSION 1.3.5 (04 April 2016)
------------------------
git reset --hard HEAD~
bash ../update_remotes.sh
add vignette/image, pump version, delete canceR.tex
git commit -m "fix vignette rm canceR.tex"
git svn rebase
git svn dcommit --add-author-from

CHANGES IN VERSION 1.3.2 (28 Mars 2016)
------------------------
Bioc devel canceR is not updated to version 1.3.1
Just add image in README

CHANGES IN VERSION 1.3.1 (24 Mars 2016)
------------------------
rewrite documents using roxygen
rewrite test package
include .travis check system

CHANGES IN VERSION 1.1.2 (12 May 2015)
------------------------
1- add Circos function to plot Menu
Function 1:    getGeneListmSigDB(): get Gene list and their gene Sets from MSigDB
Function 1.1: dialoggetGeneListMSigDB(): Select Gene Sets from list and extract hem genes

Function 2: getListProfData(): This function save Profiles Data of cancer in lists;
            Outputs:myGlobalEnv$ListProfData$Expression 
                    myGlobalEnv$ListProfData$CNA    
                    myGlobalEnv$ListMetData$HM450$StudiesRef
                    myGlobalEnv$ListMetData$HM27$StudiesRef
                    myGlobalEnv$ListProfData$RPPA$StudiesRef
                    myGlobalEnv$ListProfData$miRNA$StudiesRef
                    myGlobalEnv$ListMutData$StudiesRef
                    myGlobalEnv$Freq_DfMutData

Function 3 : getCircos(dimension="All"): Main fucntion of Circos plot: plot Tracks        
            (dimensions) and Sectors (diseases)
Function 3.1: getCor_ExpCNAMet(ListMatrix, dimension)
Function 3.2: dialogOptionCircos(): specifing which dimension and Threshold gene 
                dimensions levels will be plot.

1- dialogMetOption(): add "Circos" argument to make the difference between getMetDataMultipleGene() and getListMetData()
2- getGeneList(): add rm("GeneListMSigDB"", envir="myGlobalEnv")

CHANGES IN VERSION 1.1.1 (27 April 2015)
------------------------
1- Survival plot
1.1 add getSurvival(Coxph) and getSurvival.Rd file
1.1 getOptionGSEAlm(s, ClinicalData): add line 105
    ### only for Survival plot
    myGlobalEnv$variable <- as.formula(sprintf("Surv(OS_MONTHS,OS_STATUS)~%s", coVariables))
1.2 cancer.latex file: add Survival plot paragraph
1.3 add image in /image folder: KM.png, Coxph.png
1.4 getCasesGenProfs(): add getSurvival in Plot menu


RELEASE 1.0.0 (17 April 2015)
-------------------------

CHANGES IN VERSION 0.99.3
-------------------------

    o getProfilesDataMultipleGenes: line 78: Test only Genetic Profiles having mRNA expression to get Profile Data.
    o  getMutData(): line 96  change .GlobalEnv to myGlobalEnv)
    o  getProfDataMultipleGenes(): line 7 add testCheckedCaseGenProf()

CHANGES IN VERSION 0.99.2
-------------------------

    o Add documentation for RUN.GSEA() function
    o Remove dependency of RSvgDevice. This package is not available for Windows OS.

CHANGES IN VERSION 0.99.1
-------------------------

    o Add examples in documents

SIGNIFICANT USER-VISIBLE CHANGES

    o Add documentation for RUN.GSEA() function

    o Remove dependency of RSvgDevice. This package is not available for Windows OS.

CHANGES IN VERSION 0.99.1
--------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Add examples in documents

NEW FEATURES

    o Package released