CHANGES IN VERSION 1.36.5 (26 February 2024)
--------------------------------------------
+ fix issues with indexing Id of Cases and Genetic Profiles
+ Update functionnnalities of GSEA
+ add an example of GCT and CSL fiiles to use in GSEA

CHANGES IN VERSION 1.36.5 (26 February 2024)
--------------------------------------------
+ fix phenoTest analysis

CHANGES IN VERSION 1.36.4 (22 February 2024)
--------------------------------------------
+ modify getCases(), getGenProfs()
+ fix get Clinical data
+ fix get Mutation data
+ fix get specific mutation
+ fix get methylation data
+ fix get Profile Data for a single gene

CHANGES IN VERSION 1.36.3 (18 February 2024)
--------------------------------------------
+ update welcome panel. get all studies

CHANGES IN VERSION 1.36.2 (05 February 2024)
--------------------------------------------
+ Start migration to the new WebAPI of cBioPortal

CHANGES IN VERSION 1.29.03 (24 April 2022)
--------------------------------------------
+ host cgdsr functions

CHANGES IN VERSION 1.29.01 (20 April 2022)
--------------------------------------------
+ get cgdsr from github

CHANGES IN VERSION 1.28.04 (12 Mars 2022)
--------------------------------------------
+ omit tcltk2

CHANGES IN VERSION 1.28.03 (07 Mars 2022)
--------------------------------------------
+ Update vignette

CHANGES IN VERSION 1.28.02 (04 Mars 2022)
--------------------------------------------
+ Add bugReports link, add Views in DESCRIPTION
+ Link HTML vignette to Help Menu
+ Link to report Issues in github

CHANGES IN VERSION 1.28.01 (03 Mars 2022)
--------------------------------------------
+ Update DESCRIPTION
+ start to convert vignette from Rnd to Rmd

CHANGES IN VERSION 1.19.05 (13 June 2019)
--------------------------------------------
+ move vignette to inst/doc

CHANGES IN VERSION 1.19.04 (09 June 2019)
--------------------------------------------
+ omit GSEAlm dependency
+ include used functions from gsealm to canceR package in gsealm.R file.

CHANGES IN VERSION 1.19.03 (08 May 2019)
--------------------------------------------
+ compress RData files to RDS and move them from /data to /extdata/rdata
+ update running examples

CHANGES IN VERSION 1.19.02 (05 May 2019)
--------------------------------------------
+ remove /extdata/gct_cls
+ do not import grDevices::quartz
+ add empty line in test functions

CHANGES IN VERSION 1.19.01 (02 May 2019)
--------------------------------------------
+ remove .txt file from /data.
+ import grDevices package
+ Adjust the vignetteEngine package

CHANGES IN VERSION 1.17.6 (30 April 2019)
--------------------------------------------
 + Remove dependency of RSvgDevice. This package is not available for Windows os.
 + Remove GSEA.1.0.R from /data folder
 
CHANGES IN VERSION 1.17.5 (25 April 2019)
--------------------------------------------
+ import from grDevice new.dev savePlot
+ remove /data/datalist
+ import RSvgDevice (not available for windows OS?)

CHANGES IN VERSION 1.17.4 (22 April 2019)
--------------------------------------------
+ modify doc for cbind.na and rbind.na functiONs

CHANGES IN VERSION 1.17.3 (21 April 2019)
--------------------------------------------
+ modify doc for cbind.na and rbind.na functiONs

CHANGES IN VERSION 1.16.1 (22 February 2019)
--------------------------------------------
+ update NEWS format

CHANGES IN VERSION 1.16.1 (22 February 2019)
--------------------------------------------
+ Change the address of cgdsr: http://www.cbioportal.org/ instead
http://www.cbioportal.org/public-portal/

CHANGES IN VERSION 1.11.01 (16 october 2018)
--------------------------------------------
+ update NEWS format file

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 Mezh+ud}
+ %\VignetteDepends{}
+ %\VignetteKeyw+rds{A Graphical User Interface for accessing and m+deling 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)
------------------------
+ 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:
                   o myGlobalEnv$ListProfData$ExpressiON 
                   o myGlobalEnv$ListProfData$CNA    
                   o myGlobalEnv$ListMetData$HM450$StudiesRef
                   o myGlobalEnv$ListMetData$HM27$StudiesRef
                   o myGlobalEnv$ListProfData$RPPA$StudiesRef
                   o myGlobalEnv$ListProfData$miRNA$StudiesRef
                   o myGlobalEnv$ListMutData$StudiesRef
                   o 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.

+  dialogMetoptiON(): add "Circos" argument to make the difference between getMetDataMultipleGene() and getListMetData()
+  getGeneList(): add rm("GeneListMSigDB"", envir="myGlobalEnv")

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


CHANGES IN VERSION 1.0.0 (17 April 2015)
-------------------------

+ Release

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

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

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

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

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

    + Add examples in documents

SIGNIFICANT USER-VISIBLE CHANGES

    + Add documentation for RUN.GSEA() functiON

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

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

SIGNIFICANT USER-VISIBLE CHANGES

    + Add examples in documents

NEW FEATURES

    + Package released
