Files in kmezhoud/canceR
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/.gitignore
R/GSEA.1.0.R
R/Match_GeneList_MSigDB.R
R/Run.GSEA.1.0.R
R/aaa.R
R/about.R
R/canceR.R
R/canceR_vignette.R
R/cbind.na.R
R/cgdsr.R
R/dialogGeneClassifier.R
R/dialogMetOption.R
R/dialogMut.R
R/dialogOptionCircos.R
R/dialogOptionGSEAlm.R
R/dialogOptionPhenoTest.R
R/dialogPlotOption_SkinCor.R
R/dialogSamplingGSEA.R
R/dialogSelectFiles_GSEA.R
R/dialogSpecificMut.R
R/dialogSummary_GSEA.R
R/dialoggetGeneListMSigDB.R
R/displayInTable.R
R/getCases.R
R/getCasesGenProfs.R
R/getCircos.R
R/getClinicData_MultipleCases.R
R/getClinicalDataMatrix.R
R/getCor_ExpCNAMet.R
R/getGCTCLSExample.R
R/getGCT_CLSfiles.R
R/getGSEAlm_Diseases.R
R/getGSEAlm_Variables.R
R/getGenProfs.R
R/getGeneExpMatrix.R
R/getGeneList.R
R/getGeneListExample.R
R/getGeneListFromMSigDB.R
R/getGenesClassifier.R
R/getGenesTree_MultipleCases.R
R/getGenesTree_SingleCase.R
R/getInTable.R
R/getListProfData.R
R/getMSigDB.R
R/getMSigDBExample.R
R/getMSigDBfile.R
R/getMegaProfData.R
R/getMetDataMultipleGenes.R
R/getMutData.R
R/getPhenoTest.R
R/getProfilesDataMultipleGenes.R
R/getProfilesDataSingleGene.R
R/getSpecificMut.R
R/getSummaryGSEA.R
R/getSurvival.R
R/getTextWin.R
R/geteSet.R
R/gsealm.R
R/modalDialog.R
R/plotModel.R
R/plot_1Gene_2GenProfs.R
R/plot_2Genes_1GenProf.R
R/rbind.na.R
R/setWorkspace.R
R/testCheckedCaseGenProf.R
README.md
canceR.Rproj
inst/canceR.html
inst/canceR_ind.html
inst/canceRs.html
inst/extdata/GSEA.1.0.R
inst/extdata/GeneList/102.txt
inst/extdata/GeneList/1021.txt
inst/extdata/GeneList/223.txt
inst/extdata/GeneList/73.txt
inst/extdata/GeneList/DNA_damage_Response.txt
inst/extdata/GeneList/Glioblastoma_RTK_Ras_PI3K_AKT_Signaling.txt
inst/extdata/GeneList/INvasion_and_Metastasis.txt
inst/extdata/GeneList/ProstateCancer_AR_and_Steroid_synthesis_enzymes.txt
inst/extdata/GeneList/ProstateCancer_DownRegulated_by_Androgen.txt
inst/extdata/MSigDB/c2.cp.reactome.v4.0.symbols.gmt
inst/extdata/MSigDB/c5.bp.v4.0.symbols.gmt
inst/extdata/gct_cls/Lung_Bost_collapsed_symbols_common_Mich_Bost.gct
inst/extdata/gct_cls/Lung_Boston.cls
inst/extdata/rdata/Circos.rds
inst/extdata/rdata/brca_tcga73genes.rds
inst/extdata/rdata/brca_tcgaClassifier223.rds
inst/extdata/rdata/brca_tcgaGSEAlm1021.rds
inst/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds
inst/extdata/rdata/prad_michPhenoTest1021.rds
inst/extdata/rdata/ucec_tcga_pubGSEA1021.rds
inst/index.html
man/CGDS.Rd
man/GSEA.Analyze.Sets.Rd
man/GSEA.ConsPlot.Rd
man/GSEA.EnrichmentScore.Rd
man/GSEA.EnrichmentScore2.Rd
man/GSEA.Gct2Frame.Rd
man/GSEA.Gct2Frame2.Rd
man/GSEA.GeneRanking.Rd
man/GSEA.HeatMapPlot.Rd
man/GSEA.HeatMapPlot2.Rd
man/GSEA.NormalizeCols.Rd
man/GSEA.NormalizeRows.Rd
man/GSEA.Rd
man/GSEA.ReadClsFile.Rd
man/GSEA.Res2Frame.Rd
man/GSEA.Threshold.Rd
man/GSEA.VarFilter.Rd
man/GSEA.write.gct.Rd
man/Match_GeneList_MSigDB.Rd
man/OLD.GSEA.EnrichmentScore.Rd
man/Run.GSEA.Rd
man/UnifyRowNames.Rd
man/about.Rd
man/canceR.Rd
man/canceR_Issue.Rd
man/canceR_Vignette.Rd
man/cbind.na.Rd
man/dialogGeneClassifier.Rd
man/dialogMetOption.Rd
man/dialogMut.Rd
man/dialogOptionCircos.Rd
man/dialogOptionGSEAlm.Rd
man/dialogOptionPhenoTest.Rd
man/dialogPlotOption_SkinCor.Rd
man/dialogSamplingGSEA.Rd
man/dialogSelectFiles_GSEA.Rd
man/dialogSpecificMut.Rd
man/dialogSummary_GSEA.Rd
man/dialoggetGeneListMSigDB.Rd
man/displayInTable.Rd
man/getCases.Rd
man/getCasesGenProfs.Rd
man/getCircos.Rd
man/getClinicData_MultipleCases.Rd
man/getClinicalDataMatrix.Rd
man/getCor_ExpCNAMet.Rd
man/getFreqMutData.Rd
man/getGCTCLSExample.Rd
man/getGCT_CLSfiles.Rd
man/getGSEAlm_Diseases.Rd
man/getGSEAlm_Variables.Rd
man/getGenProfs.Rd
man/getGeneExpMatrix.Rd
man/getGeneList.Rd
man/getGeneListExample.Rd
man/getGeneListFromMSigDB.Rd
man/getGenesClassifier.Rd
man/getGenesTree_MultipleCases.Rd
man/getGenesTree_SingleCase.Rd
man/getInTable.Rd
man/getListProfData.Rd
man/getMSigDB.Rd
man/getMSigDBExample.Rd
man/getMSigDBfile.Rd
man/getMegaProfData.Rd
man/getMetDataMultipleGenes.Rd
man/getMutData.Rd
man/getPhenoTest.Rd
man/getProfData.Rd
man/getProfilesDataMultipleGenes.Rd
man/getProfilesDataSingleGene.Rd
man/getSpecificMut.Rd
man/getSummaryGSEA.Rd
man/getSurvival.Rd
man/getTextWin.Rd
man/geteSet.Rd
man/modalDialog.Rd
man/myGlobalEnv.Rd
man/plotModel.Rd
man/plot_1Gene_2GenProfs.Rd
man/plot_2Genes_1GenProf.Rd
man/rbind.na.Rd
man/setWorkspace.Rd
man/test.CGDS.Rd
man/testCheckedCaseGenProf.Rd
tests/testthat.R
tests/testthat/test_funs.R
vignettes/canceR.Rmd
vignettes/canceR.bib
vignettes/image/BrstPrstGSEAlm.png
vignettes/image/BrstPrstGSEAlm1.jpeg
vignettes/image/BrstPrstGSEAlm2.jpeg
vignettes/image/BrstPrstGSEAlm3.jpeg
vignettes/image/BrstPrstGSEAlm4.jpeg
vignettes/image/Circos.png
vignettes/image/Coxph.png
vignettes/image/GSEA-R.png
vignettes/image/GSEA-R1.jpeg
vignettes/image/GSEA-R2.jpeg
vignettes/image/GSEA-R3.jpeg
vignettes/image/GSEA-R4.jpeg
vignettes/image/GSEA-R5.jpeg
vignettes/image/GSEA-R_1.png
vignettes/image/GSEAgctcls.jpeg
vignettes/image/GSEAgctcls2.jpeg
vignettes/image/GSEAgctcls3.jpeg
vignettes/image/GeneListFromMSigDB.png
vignettes/image/GenePhenoClass1.png
vignettes/image/GenePhenoClass2.png
vignettes/image/GenePhenoClass3.png
vignettes/image/GenesClass.png
vignettes/image/GenesClass1.jpeg
vignettes/image/GenesClass2.jpg
vignettes/image/GenesClass3.jpeg
vignettes/image/GenesClass4.jpeg
vignettes/image/GenesClass5.png
vignettes/image/GenesClass6.jpeg
vignettes/image/GenesPhenoClass1.jpeg
vignettes/image/GenesPhenoClass10.jpeg
vignettes/image/GenesPhenoClass2.jpeg
vignettes/image/GenesPhenoClass3.jpeg
vignettes/image/GenesPhenoClass4.png
vignettes/image/GenesPhenoClass5.jpeg
vignettes/image/GenesPhenoClass6.jpeg
vignettes/image/GenesPhenoClass7.jpeg
vignettes/image/GenesPhenoClass8.jpeg
vignettes/image/GenesPhenoClass9.jpeg
vignettes/image/KM.png
vignettes/image/LungNatureResults.png
vignettes/image/LungNatureResults0.jpeg
vignettes/image/LungNatureResults1.jpeg
vignettes/image/MultipleProfileResult.jpeg
vignettes/image/MultipleProfileResultTree.jpeg
vignettes/image/MultipleProfileResultopen.jpeg
vignettes/image/Mutation.jpeg
vignettes/image/Mutation1.png
vignettes/image/MutationDialog.jpeg
vignettes/image/MutationResult.jpeg
vignettes/image/ProfileDialog.jpeg
vignettes/image/RHcloud.jpeg
vignettes/image/SpecificMutationDialog.jpeg
vignettes/image/breastGSEA-R1.jpeg
vignettes/image/breastGSEA-R2.jpeg
vignettes/image/breastGSEA-R3.jpeg
vignettes/image/breastGSEA.png
vignettes/image/breastGSEAlm2.jpeg
vignettes/image/clinicalData.jpeg
vignettes/image/clinicalData.png
vignettes/image/clinicalDataDialog.png
vignettes/image/dialogCircos.png
vignettes/image/gct_cls.png
vignettes/image/helpMenu.jpeg
vignettes/image/heterogeneous1.jpeg
vignettes/image/mainWindow.png
vignettes/image/methylation.png
vignettes/image/methylationDialog.jpeg
vignettes/image/methylationResult.jpeg
vignettes/image/methylationResult.png
vignettes/image/multipleProfiles.png
vignettes/image/mutation.png
vignettes/image/plot.png
vignettes/image/plot1.jpeg
vignettes/image/plot1.png
vignettes/image/plot2.jpeg
vignettes/image/plot2.jpg
vignettes/image/plot3.jpeg
vignettes/image/pradGSEAlm.png
vignettes/image/pradGSEAlm0.jpeg
vignettes/image/pradGSEAlm1.jpeg
vignettes/image/pradGSEAlm2.jpeg
vignettes/image/pradGSEAlm3.jpeg
vignettes/image/pradGSEAlm4.jpeg
vignettes/image/prad_MichiganResults.png
vignettes/image/prad_MichiganResults0.jpeg
vignettes/image/prad_MichiganResults1.jpeg
vignettes/image/prad_MichiganResults2.jpeg
vignettes/image/prad_broad-2013Results.png
vignettes/image/selectgeneList.png
vignettes/image/setWorkspace.jpeg
vignettes/image/singleProfile.png
vignettes/image/singleProfileCheckBox.jpeg
vignettes/image/singleProfileResult.jpeg
vignettes/image/specificMutation.png
vignettes/image/sradGSEAlm2.jpeg
vignettes/image/stadGSEAlm.png
vignettes/image/stadGSEAlm1.jpeg
vignettes/image/stadGSEAlm10.jpeg
vignettes/image/stadGSEAlm2.jpeg
vignettes/image/stadGSEAlm3.jpeg
vignettes/image/stadGSEAlm4.jpeg
vignettes/image/stadGSEAlm5.jpeg
vignettes/image/stadGSEAlm6.jpeg
vignettes/image/stadGSEAlm7.jpeg
vignettes/image/stadGSEAlm8.jpeg
vignettes/image/stadGSEAlm9.jpeg
vignettes/image/stadGSEAlmCNA.png
vignettes/image/starting.png
vignettes/image/startingWindow.jpeg
vignettes/image/whichMSigDB.png
vignettes/image/whichMSigDB1.jpeg
vignettes/image/whichMSigDB2.jpeg
vignettes/image/workspace.png
