CHANGES IN VERSION 1.36.8 (12 April 2024) -------------------------------------------- + update Docs 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