NEWS

---

canceR 1.36.5

• 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
• fix phenoTest analysis

canceR 1.36.4

• 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

canceR 1.36.3

• update welcome panel. get all studies

canceR 1.36.2

• Start migration to the new WebAPI of cBioPortal

canceR 1.29.03

• host cgdsr functions

canceR 1.29.01

• get cgdsr from github

canceR 1.28.04

• omit tcltk2

canceR 1.28.03

• Update vignette

canceR 1.28.02

• Add bugReports link, add Views in DESCRIPTION
• Link HTML vignette to Help Menu
• Link to report Issues in github

canceR 1.28.01

• Update DESCRIPTION
• start to convert vignette from Rnd to Rmd

canceR 1.19.05

• move vignette to inst/doc

canceR 1.19.04

• omit GSEAlm dependency
• include used functions from gsealm to canceR package in gsealm.R file.

canceR 1.19.03

• compress RData files to RDS and move them from /data to /extdata/rdata
• update running examples

canceR 1.19.02

• remove /extdata/gct_cls
• do not import grDevices::quartz
• add empty line in test functions

canceR 1.19.01

• remove .txt file from /data.
• import grDevices package
• Adjust the vignetteEngine package

canceR 1.17.6

• Remove dependency of RSvgDevice. This package is not available for Windows os.
• Remove GSEA.1.0.R from /data folder

canceR 1.17.5

• import from grDevice new.dev savePlot
• remove /data/datalist
• import RSvgDevice (not available for windows OS?)

canceR 1.17.4

• modify doc for cbind.na and rbind.na functiONs

canceR 1.17.3

• modify doc for cbind.na and rbind.na functiONs

canceR 1.16.1

• update NEWS format
• Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/

canceR 1.11.01

• update NEWS format file
• rm gamma = 1.5 argument for grDevices::rainbow functiON

canceR 1.7.04

• get Manual from Bioconductor.org
• browseURL('http://www.biocONductor.org/packages/3.4/bioc/vignettes/canceR/inst/doc/canceR.pdf')

canceR 1.7.3

• dontrun examples

canceR 1.7.2

• resolve issue when computing mutatiON frequency

canceR 1.5.2

• resolve issue 1 about "tl not found"
• delete file R/getGeneticProfiles.R
• resolve 'no visible binding for global variable'
• add R/aaa.R

canceR 1.3.91

• 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}

canceR 1.3.7

• add /extdata/canceR.pdf

canceR 1.3.6

• fix paths in running examples

canceR 1.3.5

• 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

canceR 1.3.2

• Bioc devel canceR is not updated to versiON 1.3.1
• Just add image in README

canceR 1.3.1

• rewrite documents using roxygen
• rewrite test package
• include .travis check system

canceR 1.1.2

• 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")

canceR 1.1.1

• 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

canceR 1.0.0

• Release

canceR 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()

canceR 0.99.2

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

canceR 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.
• Add examples in documents
• Package released