canceR: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.
Version 1.8.0

The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

AuthorKarim Mezhoud. Nuclear Safety & Security Department. Nuclear Science Center of Tunisia.
Bioconductor views GUI GeneExpression Software
Date of publicationNone
MaintainerKarim Mezhoud <kmezhoud@gmail.com>
LicenseGPL-2
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("canceR")

Getting started

README.md

Popular man pages

dialogGeneClassifier: Dialogue Box for gene classifier setting: sample size and...
dialogOptionCircos: Checkbox to select dimensions
getSpecificMut: get specific Mutation data for multiple genes
getTextWin: get text in tcltk windows
GSEA: GSEA-R (Broad Institute)
GSEA.Gct2Frame2: GSEA.Gct2Frame2
plot_1Gene_2GenProfs: Plotting two genetic profiles for one Gene
See all...

All man pages Function index File listing

Man pages

about: about canceR
canceR: main function
canceRHelp: canceR Help
canceR_Vignette: open pdf vignette
cbind.na: bind non equal colunm
ClinicalData: ClinicalData
dialogGeneClassifier: Dialogue Box for gene classifier setting: sample size and...
dialoggetGeneListMSigDB: Multi-select choice of gene sets from loaded MSigDB
dialogMetOption: Dialog Box to set methylation options
dialogMut: Dialog bos to set returned Mutation information
dialogOptionCircos: Checkbox to select dimensions
dialogOptionGSEAlm: Dialogbox to select variables from Clinical data
dialogOptionPhenoTest: Checkbox to select variables from clinical data
dialogPlotOption_SkinCor: Checkbox to select variables for plotting
dialogSamplingGSEA: Dialog Box for Sampling patients from expression profile data...
dialogSelectFiles_GSEA: Dialog Box to Select GCT, CLS, GMT and output Files for...
dialogSpecificMut: dialog box to Specify Mutation using Regular Expression....
dialogSummary_GSEA: Dialog Box to specify phenotype (variable) used in last...
displayInTable: Display matrix in tcltk table
GeneExpMatrix: GeneExpMatrix
getCases: Get cases for selected Studies. The Cases are the descrption...
getCasesGenProfs: get Cases and Genetic Profiles of selected Studies.
getCircos: get Circos Layout for selected studies and selected...
getClinicalDataMatrix: get matrix with clinical from file
getClinicData_MultipleCases: get Clinical Data for Multiple Cases. User needs to select at...
getCor_ExpCNAMet: Get gene correlation for multiple dimensions.
geteSet: Built Expression Set (eSet) from profile data.
getGCTCLSExample: get GCT and CLS example files.
getGCT_CLSfiles: get Profile (GCT file) and Phenotype (CLS file) Data from...
getGeneExpMatrix: get matrix with gene expression from file
getGeneList: User needs to specify which gene is interesting to get...
getGeneListExample: get Gene List from examples. User can select one from...
getGeneListFromMSigDB: get gene list from MSigDB
getGenesClassifier: get Genes Classifier
getGenesTree_MultipleCases: Get successively trees of genes list for multiple cases
getGenesTree_SingleCase: classify genes in tree for two phenotypes in the same...
getGenProfs: Get Genetic Profile from selected Studies
getGSEAlm_Diseases: get GSEA linear modeling by studies (diseases)
getGSEAlm_Variables: get GSEA linear modeling by variables (phenotype)
getInTable: get dataframe in TK/TCL table
getListProfData: get a list of Profile Data of every available dimensions....
getMegaProfData: Get profile data for more than 500 genes list.
getMetDataMultipleGenes: get Methylation data for multiple genes
getMSigDB: Reduce MSigDB size for only gene list
getMSigDBExample: get example of .gmt file from MSigDB (Broad Institute)
getMSigDBfile: Dialog Box to Select MSigDB Files from drive
getMutData: get Mutation data for multiple genes
getPhenoTest: Associate phenotype to Studies (cancers)
getProfilesDataMultipleGenes: get Profles Data of multiple genes
getProfilesDataSingleGene: get Profiles Data for a Single Gene.
getSpecificMut: get specific Mutation data for multiple genes
getSummaryGSEA: get Summary results from GSEA-R (Broad Institute)
getSurvival: Survival plot
getTextWin: get text in tcltk windows
GSEA: GSEA-R (Broad Institute)
GSEA.Analyze.Sets: GSEA.Analyze.Sets
GSEA.ConsPlot: GSEA.ConsPlot
GSEA.EnrichmentScore: GSEA.EnrichmentScore
GSEA.EnrichmentScore2: GSEA.EnrichmentScore2
GSEA.Gct2Frame: GSEA.Gct2Frame
GSEA.Gct2Frame2: GSEA.Gct2Frame2
GSEA.GeneRanking: GSEA.GeneRanking
GSEA.HeatMapPlot: GSEA.HeatMapPlot
GSEA.HeatMapPlot2: GSEA.HeatMapPlot2
GSEA.NormalizeCols: GSEA.NormalizeCols
GSEA.NormalizeRows: GSEA.NormalizeRows
GSEA.ReadClsFile: GSEA.ReadClsFile
GSEA.Res2Frame: GSEA.Res2Frame
GSEA.Threshold: GSEA.Threshold
GSEA.VarFilter: GSEA.VarFilter
GSEA.write.gct: GSEA.write.gct
Match_GeneList_MSigDB: Search MSigDb that overlap gene list
modalDialog: Dialog box to specify Gene Symbol.
myGlobalEnv: myGlobalEnv
OLD.GSEA.EnrichmentScore: OLD.GSEA.EnrichmentScore
plot_1Gene_2GenProfs: Plotting two genetic profiles for one Gene
plot_2Genes_1GenProf: plot correlation of two genes expressions.
plotModel: model plotting with tcltk
rbind.na: bind non equal row
Run.GSEA: The main function to run GSEA-R from Broad Institute
setWorkspace: Setting work Directory and output folders.At starting window,...
testCheckedCaseGenProf: Testing checked appropriate Cases for appropriate Genetic...

Functions

ClinicalData Man page
GSEA Man page Source code
GSEA.Analyze.Sets Man page Source code
GSEA.ConsPlot Man page Source code
GSEA.EnrichmentScore Man page Source code
GSEA.EnrichmentScore2 Man page Source code
GSEA.Gct2Frame Man page Source code
GSEA.Gct2Frame2 Man page Source code
GSEA.GeneRanking Man page Source code
GSEA.HeatMapPlot Man page Source code
GSEA.HeatMapPlot2 Man page Source code
GSEA.NormalizeCols Man page Source code
GSEA.NormalizeRows Man page Source code
GSEA.ReadClsFile Man page Source code
GSEA.Res2Frame Man page Source code
GSEA.Threshold Man page Source code
GSEA.VarFilter Man page Source code
GSEA.write.gct Man page Source code
GeneExpMatrix Man page
Match_GeneList_MSigDB Man page Source code
OLD.GSEA.EnrichmentScore Man page Source code
Run.GSEA Man page Source code
about Man page Source code
canceR Man page Source code
canceRHelp Man page
canceR_Vignette Man page
cbind.na Man page Source code
dialogGeneClassifier Man page Source code
dialogMetOption Man page Source code
dialogMut Man page Source code
dialogOptionCircos Man page Source code
dialogOptionGSEAlm Man page Source code
dialogOptionPhenoTest Man page Source code
dialogPlotOption_SkinCor Man page Source code
dialogSamplingGSEA Man page Source code
dialogSelectFiles_GSEA Man page Source code
dialogSpecificMut Man page Source code
dialogSummary_GSEA Man page Source code
dialoggetGeneListMSigDB Man page Source code
displayInTable Man page Source code
getCases Man page Source code
getCasesGenProfs Man page Source code
getCircos Man page Source code
getClinicData_MultipleCases Man page Source code
getClinicalDataMatrix Man page Source code
getCor_ExpCNAMet Man page Source code
getGCTCLSExample Man page Source code
getGCT_CLSfiles Man page Source code
getGSEAlm_Diseases Man page Source code
getGSEAlm_Variables Man page Source code
getGenProfs Man page Source code
getGeneExpMatrix Man page Source code
getGeneList Man page Source code
getGeneListExample Man page Source code
getGeneListFromMSigDB Man page Source code
getGenesClassifier Man page Source code
getGenesTree_MultipleCases Man page Source code
getGenesTree_SingleCase Man page Source code
getInTable Man page Source code
getListProfData Man page Source code
getMSigDB Man page Source code
getMSigDBExample Man page Source code
getMSigDBfile Man page Source code
getMegaProfData Man page Source code
getMetDataMultipleGenes Man page Source code
getMutData Man page Source code
getPhenoTest Man page Source code
getProfilesDataMultipleGenes Man page Source code
getProfilesDataSingleGene Man page Source code
getSpecificMut Man page Source code
getSummaryGSEA Man page Source code
getSurvival Man page Source code
getTextWin Man page Source code
geteSet Man page Source code
modalDialog Man page Source code
myGlobalEnv Man page
plotModel Man page Source code
plot_1Gene_2GenProfs Man page Source code
plot_2Genes_1GenProf Man page Source code
rbind.na Man page Source code
setWorkspace Man page Source code
testCheckedCaseGenProf Man page Source code

Files

.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R
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/canceRHelp.R
R/canceR_pdf.R
R/cbind.na.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/getGeneticProfiles.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/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
build
build/vignette.rds
canceR.Rproj
data
data/Circos.RData
data/ClinicalData.txt
data/GSEA.1.0.R
data/GeneExpMatrix.txt
data/brca_tcga73genes.RData
data/brca_tcgaClassifier223.RData
data/brca_tcgaGSEAlm1021.RData
data/datalist
data/datalist/ClinicalData.txt
data/gbm_tcgaPlotTwoGenProf.RData
data/prad_michPhenoTest1021.RData
data/ucec_tcga_pubGSEA1021.RData
inst
inst/canceR.html
inst/canceR_ind.html
inst/canceRs.html
inst/doc
inst/doc/canceR.Rnw
inst/doc/canceR.pdf
inst/extdata
inst/extdata/GeneList
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
inst/extdata/MSigDB/c2.cp.reactome.v4.0.symbols.gmt
inst/extdata/MSigDB/c5.bp.v4.0.symbols.gmt
inst/extdata/gct_cls
inst/extdata/gct_cls/Lung_Bost_collapsed_symbols_common_Mich_Bost.gct
inst/extdata/gct_cls/Lung_Boston.cls
inst/index.html
man
man/ClinicalData.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/GeneExpMatrix.Rd
man/Match_GeneList_MSigDB.Rd
man/OLD.GSEA.EnrichmentScore.Rd
man/Run.GSEA.Rd
man/about.Rd
man/canceR.Rd
man/canceRHelp.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/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/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/testCheckedCaseGenProf.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_funs.R
vignettes
vignettes/canceR.Rnw
vignettes/canceR.bib
vignettes/image
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/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/prad_broad-2013Results0.jpeg
vignettes/image/prad_broad-2013Results1.jpeg
vignettes/image/prad_broad-2013Results2.jpeg
vignettes/image/prad_broad-2013Results3.jpeg
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/starting.svg
vignettes/image/startingWindow.jpeg
vignettes/image/whichMSigDB.png
vignettes/image/whichMSigDB1.jpeg
vignettes/image/whichMSigDB2.jpeg
vignettes/image/workspace.png
canceR documentation built on May 20, 2017, 9:32 p.m.