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

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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).

Author
Karim Mezhoud. Nuclear Safety & Security Department. Nuclear Science Center of Tunisia.
Date of publication
None
Maintainer
Karim Mezhoud <kmezhoud@gmail.com>
License
GPL-2
Version
1.6.0

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...

Files in this package

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