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

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.
Date of publicationNone
MaintainerKarim Mezhoud <kmezhoud@gmail.com>
LicenseGPL-2
Version1.6.0

View on Bioconductor

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

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

Files

canceR/.travis.yml
canceR/DESCRIPTION
canceR/NAMESPACE
canceR/NEWS
canceR/R
canceR/R/GSEA.1.0.R canceR/R/Match_GeneList_MSigDB.R canceR/R/Run.GSEA.1.0.R canceR/R/about.R canceR/R/canceR.R canceR/R/canceRHelp.R canceR/R/canceR_pdf.R canceR/R/cbind.na.R canceR/R/dialogGeneClassifier.R canceR/R/dialogMetOption.R canceR/R/dialogMut.R canceR/R/dialogOptionCircos.R canceR/R/dialogOptionGSEAlm.R canceR/R/dialogOptionPhenoTest.R canceR/R/dialogPlotOption_SkinCor.R canceR/R/dialogSamplingGSEA.R canceR/R/dialogSelectFiles_GSEA.R canceR/R/dialogSpecificMut.R canceR/R/dialogSummary_GSEA.R canceR/R/dialoggetGeneListMSigDB.R canceR/R/displayInTable.R canceR/R/getCases.R canceR/R/getCasesGenProfs.R canceR/R/getCircos.R canceR/R/getClinicData_MultipleCases.R canceR/R/getClinicalDataMatrix.R canceR/R/getCor_ExpCNAMet.R canceR/R/getGCTCLSExample.R canceR/R/getGCT_CLSfiles.R canceR/R/getGSEAlm_Diseases.R canceR/R/getGSEAlm_Variables.R canceR/R/getGenProfs.R canceR/R/getGeneExpMatrix.R canceR/R/getGeneList.R canceR/R/getGeneListExample.R canceR/R/getGeneListFromMSigDB.R canceR/R/getGenesClassifier.R canceR/R/getGenesTree_MultipleCases.R canceR/R/getGenesTree_SingleCase.R canceR/R/getGeneticProfiles.R canceR/R/getInTable.R canceR/R/getListProfData.R canceR/R/getMSigDB.R canceR/R/getMSigDBExample.R canceR/R/getMSigDBfile.R canceR/R/getMegaProfData.R canceR/R/getMetDataMultipleGenes.R canceR/R/getMutData.R canceR/R/getPhenoTest.R canceR/R/getProfilesDataMultipleGenes.R canceR/R/getProfilesDataSingleGene.R canceR/R/getSpecificMut.R canceR/R/getSummaryGSEA.R canceR/R/getSurvival.R canceR/R/getTextWin.R canceR/R/geteSet.R canceR/R/modalDialog.R canceR/R/plotModel.R canceR/R/plot_1Gene_2GenProfs.R canceR/R/plot_2Genes_1GenProf.R canceR/R/rbind.na.R canceR/R/setWorkspace.R canceR/R/testCheckedCaseGenProf.R
canceR/README.md
canceR/build
canceR/build/vignette.rds
canceR/canceR.Rproj
canceR/data
canceR/data/Circos.RData
canceR/data/ClinicalData.txt
canceR/data/GSEA.1.0.R
canceR/data/GeneExpMatrix.txt
canceR/data/brca_tcga73genes.RData
canceR/data/brca_tcgaClassifier223.RData
canceR/data/brca_tcgaGSEAlm1021.RData
canceR/data/datalist
canceR/data/datalist/ClinicalData.txt
canceR/data/gbm_tcgaPlotTwoGenProf.RData
canceR/data/prad_michPhenoTest1021.RData
canceR/data/ucec_tcga_pubGSEA1021.RData
canceR/inst
canceR/inst/canceR.html
canceR/inst/canceR_ind.html
canceR/inst/canceRs.html
canceR/inst/doc
canceR/inst/doc/canceR.Rnw
canceR/inst/doc/canceR.pdf
canceR/inst/extdata
canceR/inst/extdata/GeneList
canceR/inst/extdata/GeneList/102.txt
canceR/inst/extdata/GeneList/1021.txt
canceR/inst/extdata/GeneList/223.txt
canceR/inst/extdata/GeneList/73.txt
canceR/inst/extdata/GeneList/DNA_damage_Response.txt
canceR/inst/extdata/GeneList/Glioblastoma_RTK_Ras_PI3K_AKT_Signaling.txt
canceR/inst/extdata/GeneList/INvasion_and_Metastasis.txt
canceR/inst/extdata/GeneList/ProstateCancer_AR_and_Steroid_synthesis_enzymes.txt
canceR/inst/extdata/GeneList/ProstateCancer_DownRegulated_by_Androgen.txt
canceR/inst/extdata/MSigDB
canceR/inst/extdata/MSigDB/c2.cp.reactome.v4.0.symbols.gmt
canceR/inst/extdata/MSigDB/c5.bp.v4.0.symbols.gmt
canceR/inst/extdata/gct_cls
canceR/inst/extdata/gct_cls/Lung_Bost_collapsed_symbols_common_Mich_Bost.gct
canceR/inst/extdata/gct_cls/Lung_Boston.cls
canceR/inst/index.html
canceR/man
canceR/man/ClinicalData.Rd canceR/man/GSEA.Analyze.Sets.Rd canceR/man/GSEA.ConsPlot.Rd canceR/man/GSEA.EnrichmentScore.Rd canceR/man/GSEA.EnrichmentScore2.Rd canceR/man/GSEA.Gct2Frame.Rd canceR/man/GSEA.Gct2Frame2.Rd canceR/man/GSEA.GeneRanking.Rd canceR/man/GSEA.HeatMapPlot.Rd canceR/man/GSEA.HeatMapPlot2.Rd canceR/man/GSEA.NormalizeCols.Rd canceR/man/GSEA.NormalizeRows.Rd canceR/man/GSEA.Rd canceR/man/GSEA.ReadClsFile.Rd canceR/man/GSEA.Res2Frame.Rd canceR/man/GSEA.Threshold.Rd canceR/man/GSEA.VarFilter.Rd canceR/man/GSEA.write.gct.Rd canceR/man/GeneExpMatrix.Rd canceR/man/Match_GeneList_MSigDB.Rd canceR/man/OLD.GSEA.EnrichmentScore.Rd canceR/man/Run.GSEA.Rd canceR/man/about.Rd canceR/man/canceR.Rd canceR/man/canceRHelp.Rd canceR/man/canceR_Vignette.Rd canceR/man/cbind.na.Rd canceR/man/dialogGeneClassifier.Rd canceR/man/dialogMetOption.Rd canceR/man/dialogMut.Rd canceR/man/dialogOptionCircos.Rd canceR/man/dialogOptionGSEAlm.Rd canceR/man/dialogOptionPhenoTest.Rd canceR/man/dialogPlotOption_SkinCor.Rd canceR/man/dialogSamplingGSEA.Rd canceR/man/dialogSelectFiles_GSEA.Rd canceR/man/dialogSpecificMut.Rd canceR/man/dialogSummary_GSEA.Rd canceR/man/dialoggetGeneListMSigDB.Rd canceR/man/displayInTable.Rd canceR/man/getCases.Rd canceR/man/getCasesGenProfs.Rd canceR/man/getCircos.Rd canceR/man/getClinicData_MultipleCases.Rd canceR/man/getClinicalDataMatrix.Rd canceR/man/getCor_ExpCNAMet.Rd canceR/man/getGCTCLSExample.Rd canceR/man/getGCT_CLSfiles.Rd canceR/man/getGSEAlm_Diseases.Rd canceR/man/getGSEAlm_Variables.Rd canceR/man/getGenProfs.Rd canceR/man/getGeneExpMatrix.Rd canceR/man/getGeneList.Rd canceR/man/getGeneListExample.Rd canceR/man/getGeneListFromMSigDB.Rd canceR/man/getGenesClassifier.Rd canceR/man/getGenesTree_MultipleCases.Rd canceR/man/getGenesTree_SingleCase.Rd canceR/man/getInTable.Rd canceR/man/getListProfData.Rd canceR/man/getMSigDB.Rd canceR/man/getMSigDBExample.Rd canceR/man/getMSigDBfile.Rd canceR/man/getMegaProfData.Rd canceR/man/getMetDataMultipleGenes.Rd canceR/man/getMutData.Rd canceR/man/getPhenoTest.Rd canceR/man/getProfilesDataMultipleGenes.Rd canceR/man/getProfilesDataSingleGene.Rd canceR/man/getSpecificMut.Rd canceR/man/getSummaryGSEA.Rd canceR/man/getSurvival.Rd canceR/man/getTextWin.Rd canceR/man/geteSet.Rd canceR/man/modalDialog.Rd canceR/man/myGlobalEnv.Rd canceR/man/plotModel.Rd canceR/man/plot_1Gene_2GenProfs.Rd canceR/man/plot_2Genes_1GenProf.Rd canceR/man/rbind.na.Rd canceR/man/setWorkspace.Rd canceR/man/testCheckedCaseGenProf.Rd
canceR/tests
canceR/tests/testthat
canceR/tests/testthat.R
canceR/tests/testthat/test_funs.R
canceR/vignettes
canceR/vignettes/canceR.Rnw
canceR/vignettes/canceR.bib
canceR/vignettes/image
canceR/vignettes/image/BrstPrstGSEAlm.png
canceR/vignettes/image/BrstPrstGSEAlm1.jpeg
canceR/vignettes/image/BrstPrstGSEAlm2.jpeg
canceR/vignettes/image/BrstPrstGSEAlm3.jpeg
canceR/vignettes/image/BrstPrstGSEAlm4.jpeg
canceR/vignettes/image/Circos.png
canceR/vignettes/image/Coxph.png
canceR/vignettes/image/GSEA-R.png
canceR/vignettes/image/GSEA-R1.jpeg
canceR/vignettes/image/GSEA-R2.jpeg
canceR/vignettes/image/GSEA-R3.jpeg
canceR/vignettes/image/GSEA-R4.jpeg
canceR/vignettes/image/GSEA-R5.jpeg
canceR/vignettes/image/GSEAgctcls.jpeg
canceR/vignettes/image/GSEAgctcls2.jpeg
canceR/vignettes/image/GSEAgctcls3.jpeg
canceR/vignettes/image/GeneListFromMSigDB.png
canceR/vignettes/image/GenePhenoClass1.png
canceR/vignettes/image/GenePhenoClass2.png
canceR/vignettes/image/GenePhenoClass3.png
canceR/vignettes/image/GenesClass.png
canceR/vignettes/image/GenesClass1.jpeg
canceR/vignettes/image/GenesClass2.jpg
canceR/vignettes/image/GenesClass3.jpeg
canceR/vignettes/image/GenesClass4.jpeg
canceR/vignettes/image/GenesClass5.png
canceR/vignettes/image/GenesClass6.jpeg
canceR/vignettes/image/GenesPhenoClass1.jpeg
canceR/vignettes/image/GenesPhenoClass10.jpeg
canceR/vignettes/image/GenesPhenoClass2.jpeg
canceR/vignettes/image/GenesPhenoClass3.jpeg
canceR/vignettes/image/GenesPhenoClass4.png
canceR/vignettes/image/GenesPhenoClass5.jpeg
canceR/vignettes/image/GenesPhenoClass6.jpeg
canceR/vignettes/image/GenesPhenoClass7.jpeg
canceR/vignettes/image/GenesPhenoClass8.jpeg
canceR/vignettes/image/GenesPhenoClass9.jpeg
canceR/vignettes/image/KM.png
canceR/vignettes/image/LungNatureResults.png
canceR/vignettes/image/LungNatureResults0.jpeg
canceR/vignettes/image/LungNatureResults1.jpeg
canceR/vignettes/image/MultipleProfileResult.jpeg
canceR/vignettes/image/MultipleProfileResultTree.jpeg
canceR/vignettes/image/MultipleProfileResultopen.jpeg
canceR/vignettes/image/Mutation.jpeg
canceR/vignettes/image/Mutation1.png
canceR/vignettes/image/MutationDialog.jpeg
canceR/vignettes/image/MutationResult.jpeg
canceR/vignettes/image/ProfileDialog.jpeg
canceR/vignettes/image/RHcloud.jpeg
canceR/vignettes/image/SpecificMutationDialog.jpeg
canceR/vignettes/image/breastGSEA-R1.jpeg
canceR/vignettes/image/breastGSEA-R2.jpeg
canceR/vignettes/image/breastGSEA-R3.jpeg
canceR/vignettes/image/breastGSEA.png
canceR/vignettes/image/breastGSEAlm2.jpeg
canceR/vignettes/image/clinicalData.jpeg
canceR/vignettes/image/clinicalData.png
canceR/vignettes/image/clinicalDataDialog.png
canceR/vignettes/image/dialogCircos.png
canceR/vignettes/image/gct_cls.png
canceR/vignettes/image/helpMenu.jpeg
canceR/vignettes/image/heterogeneous1.jpeg
canceR/vignettes/image/mainWindow.png
canceR/vignettes/image/methylation.png
canceR/vignettes/image/methylationDialog.jpeg
canceR/vignettes/image/methylationResult.jpeg
canceR/vignettes/image/methylationResult.png
canceR/vignettes/image/multipleProfiles.png
canceR/vignettes/image/mutation.png
canceR/vignettes/image/plot.png
canceR/vignettes/image/plot1.jpeg
canceR/vignettes/image/plot1.png
canceR/vignettes/image/plot2.jpeg
canceR/vignettes/image/plot2.jpg
canceR/vignettes/image/plot3.jpeg
canceR/vignettes/image/pradGSEAlm.png
canceR/vignettes/image/pradGSEAlm0.jpeg
canceR/vignettes/image/pradGSEAlm1.jpeg
canceR/vignettes/image/pradGSEAlm2.jpeg
canceR/vignettes/image/pradGSEAlm3.jpeg
canceR/vignettes/image/pradGSEAlm4.jpeg
canceR/vignettes/image/prad_MichiganResults.png
canceR/vignettes/image/prad_MichiganResults0.jpeg
canceR/vignettes/image/prad_MichiganResults1.jpeg
canceR/vignettes/image/prad_MichiganResults2.jpeg
canceR/vignettes/image/prad_broad-2013Results.png
canceR/vignettes/image/prad_broad-2013Results0.jpeg
canceR/vignettes/image/prad_broad-2013Results1.jpeg
canceR/vignettes/image/prad_broad-2013Results2.jpeg
canceR/vignettes/image/prad_broad-2013Results3.jpeg
canceR/vignettes/image/selectgeneList.png
canceR/vignettes/image/setWorkspace.jpeg
canceR/vignettes/image/singleProfile.png
canceR/vignettes/image/singleProfileCheckBox.jpeg
canceR/vignettes/image/singleProfileResult.jpeg
canceR/vignettes/image/specificMutation.png
canceR/vignettes/image/sradGSEAlm2.jpeg
canceR/vignettes/image/stadGSEAlm.png
canceR/vignettes/image/stadGSEAlm1.jpeg
canceR/vignettes/image/stadGSEAlm10.jpeg
canceR/vignettes/image/stadGSEAlm2.jpeg
canceR/vignettes/image/stadGSEAlm3.jpeg
canceR/vignettes/image/stadGSEAlm4.jpeg
canceR/vignettes/image/stadGSEAlm5.jpeg
canceR/vignettes/image/stadGSEAlm6.jpeg
canceR/vignettes/image/stadGSEAlm7.jpeg
canceR/vignettes/image/stadGSEAlm8.jpeg
canceR/vignettes/image/stadGSEAlm9.jpeg
canceR/vignettes/image/stadGSEAlmCNA.png
canceR/vignettes/image/starting.png
canceR/vignettes/image/starting.svg
canceR/vignettes/image/startingWindow.jpeg
canceR/vignettes/image/whichMSigDB.png
canceR/vignettes/image/whichMSigDB1.jpeg
canceR/vignettes/image/whichMSigDB2.jpeg
canceR/vignettes/image/workspace.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.