Changes in version 1.36.5 o fix issues with indexing Id of Cases and Genetic Profiles o Update functionnnalities of GSEA o add an example of GCT and CSL fiiles to use in GSEA o fix phenoTest analysis Changes in version 1.36.4 o modify getCases(), getGenProfs() o fix get Clinical data o fix get Mutation data o fix get specific mutation o fix get methylation data o fix get Profile Data for a single gene Changes in version 1.36.3 o update welcome panel. get all studies Changes in version 1.36.2 o Start migration to the new WebAPI of cBioPortal Changes in version 1.29.03 o host cgdsr functions Changes in version 1.29.01 o get cgdsr from github Changes in version 1.28.04 o omit tcltk2 Changes in version 1.28.03 o Update vignette Changes in version 1.28.02 o Add bugReports link, add Views in DESCRIPTION o Link HTML vignette to Help Menu o Link to report Issues in github Changes in version 1.28.01 o Update DESCRIPTION o start to convert vignette from Rnd to Rmd Changes in version 1.19.05 o move vignette to inst/doc Changes in version 1.19.04 o omit GSEAlm dependency o include used functions from gsealm to canceR package in gsealm.R file. Changes in version 1.19.03 o compress RData files to RDS and move them from /data to /extdata/rdata o update running examples Changes in version 1.19.02 o remove /extdata/gct_cls o do not import grDevices::quartz o add empty line in test functions Changes in version 1.19.01 o remove .txt file from /data. o import grDevices package o Adjust the vignetteEngine package Changes in version 1.17.6 o Remove dependency of RSvgDevice. This package is not available for Windows os. o Remove GSEA.1.0.R from /data folder Changes in version 1.17.5 o import from grDevice new.dev savePlot o remove /data/datalist o import RSvgDevice (not available for windows OS?) Changes in version 1.17.4 o modify doc for cbind.na and rbind.na functiONs Changes in version 1.17.3 o modify doc for cbind.na and rbind.na functiONs Changes in version 1.16.1 o update NEWS format o Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/ Changes in version 1.11.01 o update NEWS format file o rm gamma = 1.5 argument for grDevices::rainbow functiON Changes in version 1.7.04 o get Manual from Bioconductor.org o browseURL('http://www.biocONductor.org/packages/3.4/bioc/vignettes/canceR/inst/doc/canceR.pdf') Changes in version 1.7.3 o dontrun examples Changes in version 1.7.2 o resolve issue when computing mutatiON frequency Changes in version 1.5.2 o resolve issue 1 about "tl not found" o delete file R/getGeneticProfiles.R o resolve 'no visible binding for global variable' o add R/aaa.R Changes in version 1.3.91 o rm canceR.pdf and lines from canceR.Rnw o %\VignetteEngine{R.rsp::tex} o %\VignetteKeyword{R} o %\VignetteKeyword{package} o %\VignetteKeyword{vignette} o %\VignetteKeyword{LaTeX} o %\VignetteAuthor{Karim Mezh+ud} o %\VignetteDepends{} o %\VignetteKeyw+rds{A Graphical User Interface for accessing and m+deling the MSKCC Cancer Genomics Data.} o %\VignettePackage{canceR} Changes in version 1.3.7 o add /extdata/canceR.pdf Changes in version 1.3.6 o fix paths in running examples Changes in version 1.3.5 o git reset --hard HEAD~ o bash ../update_remotes.sh o add vignette/image, pump version, delete canceR.tex o git commit -m "fix vignette rm canceR.tex" o git svn rebase o git svn dcommit --add-author-from Changes in version 1.3.2 o Bioc devel canceR is not updated to versiON 1.3.1 o Just add image in README Changes in version 1.3.1 o rewrite documents using roxygen o rewrite test package o include .travis check system Changes in version 1.1.2 o add Circos functiON to plot Menu o Function 1: getGeneListmSigDB(): get Gene list and their gene Sets from MSigDB o Function 1.1: dialoggetGeneListMSigDB(): Select Gene Sets from list and extract hem genes o 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$Freq_DfMutData o FunctiON 3 : getCircos(dimensiON="All"): Main fucntiON of Circos plot: plot Tracks (dimensiONs) and Sectors (diseases) o FunctiON 3.1: getCor_ExpCNAMet(ListMatrix, dimensiON) o FunctiON 3.2: dialogoptiONCircos(): specifing which dimensiON and Threshold gene dimensiONs levels will be plot. o dialogMetoptiON(): add "Circos" argument to make the difference between getMetDataMultipleGene() and getListMetData() o getGeneList(): add rm("GeneListMSigDB"", envir="myGlobalEnv") Changes in version 1.1.1 o Survival plot o add getSurvival(Coxph) and getSurvival.Rd file o getoptiONGSEAlm(s, ClinicalData): add line 105 - ###ONly for Survival plot - myGlobalEnv$variable <- as.formula(sprintf("Surv(OS_MONTHS,OS_STATUS)~%s", coVariables)) o cancer.latex file: add Survival plot paragraph o add image in /image folder: KM.png, Coxph.png o getCasesGenProfs(): add getSurvival in Plot menu Changes in version 1.0.0 o Release 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. o Add examples in documents o Package released