Package: canceR 1.41.0

Karim Mezhoud

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).

Authors:Karim Mezhoud. Nuclear Safety & Security Department. Nuclear Science Center of Tunisia.

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canceR.pdf |canceR.html✨
canceR/json (API)
NEWS

# Install 'canceR' in R:
install.packages('canceR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kmezhoud/cancer/issues

On BioConductor:canceR-1.39.0(bioc 3.20)canceR-1.38.0(bioc 3.19)

guigeneexpressionclusteringgogenesetenrichmentkeggmultiplecomparisoncancercancer-datagenegene-expressiongene-methylationgene-mutationgene-setsmethylationmskccmutationstcltk

5.25 score 7 stars 17 scripts 261 downloads 62 exports 204 dependencies

Last updated 2 months agofrom:89371a8f57. Checks:OK: 1 WARNING: 2 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:aboutcanceRcanceR_IssuecanceR_VignetteCGDSdialogGeneClassifierdialoggetGeneListMSigDBdialogMetOptiondialogMutdialogOptionCircosdialogOptionGSEAlmdialogOptionPhenoTestdialogPlotOption_SkinCordialogSamplingGSEAdialogSelectFiles_GSEAdialogSpecificMutdialogSummary_GSEAdisplayInTablegetCasesgetCasesGenProfsgetCircosgetClinicalDataMatrixgetClinicData_MultipleCasesgeteSetgetFreqMutDatagetGCT_CLSfilesgetGCTCLSExamplegetGeneExpMatrixgetGeneListgetGeneListExamplegetGeneListFromMSigDBgetGenesClassifiergetGenesTree_MultipleCasesgetGenesTree_SingleCasegetGenProfsgetGSEAlm_DiseasesgetGSEAlm_VariablesgetInTablegetMegaProfDatagetMetDataMultipleGenesgetMSigDBgetMSigDBExamplegetMSigDBfilegetMutDatagetPhenoTestgetProfDatagetProfilesDataMultipleGenesgetProfilesDataSingleGenegetSpecificMutgetSummaryGSEAgetSurvivalgetTextWinMatch_GeneList_MSigDBmodalDialogplot_1Gene_2GenProfsplot_2Genes_1GenProfplotModelRun.GSEAsetWorkspacetest.CGDStestCheckedCaseGenProfUnifyRowNames

Dependencies:abindannotateAnnotationDbiAnVILAnVILBaseaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobBMAbslibcachemCategorycaToolscBioPortalDatacheckmatecirclizeclassclicliprclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDEoptimRdigestdplyrDTe1071EBarraysellipseevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsgeNetClassifierGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesggplot2GlobalOptionsgluegplotsgraphgridExtraGSEABasegtablegtoolsHeatplushgu133a.dbhighrHmischmshopachhtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2infotheoinlineIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminetminiUIMultiAssayExperimentmunsellmvtnormnlmennetopensslorg.Hs.eg.dbpcaPPphenoTestpillarpkgconfigplogrplyrpngprettyunitsprogresspromisesproxypurrrR.methodsS3R.ooR6RaggedExperimentrapiclientrappdirsRBGLRColorBrewerRcppRCurlreadrrestfulrRhtslibrjsonRJSONIOrlangrmarkdownrobustbaserpartrrcovRsamtoolsRSQLiterstudioapiRTCGAToolboxrtracklayerRUnitrvestS4ArraysS4VectorssassscalesselectrshapeshinysnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsurvivalsysTCGAutilstibbletidyrtidyselecttinytextkrplottzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc

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

Karim Mezhoud

Rendered fromcanceR.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-04-24
Started: 2022-04-24

Readme and manuals

Help Manual

Help pageTopics
about canceRabout
main functioncanceR
canceR Report IssuecanceR_Issue
open pdf vignettecanceR_Vignette
bind non equal colunmcbind.na
CGDS connect object to cBioPortalCGDS
Dialogue Box for gene classifier setting: sample size and postprob thresholddialogGeneClassifier
Multi-select choice of gene sets from loaded MSigDBdialoggetGeneListMSigDB
Dialog Box to set methylation optionsdialogMetOption
Dialog bos to set returned Mutation informationdialogMut
Checkbox to select dimensionsdialogOptionCircos
Dialogbox to select variables from Clinical datadialogOptionGSEAlm
Checkbox to select variables from clinical datadialogOptionPhenoTest
Checkbox to select variables for plottingdialogPlotOption_SkinCor
Dialog Box for Sampling patients from expression profile data used for GSEA-R (Broad Institute)dialogSamplingGSEA
Dialog Box to Select GCT, CLS, GMT and output Files for GSEA-R (Broad Institute)dialogSelectFiles_GSEA
dialog box to Specify Mutation using Regular Expression. Search specific mutation using regular expression.dialogSpecificMut
Dialog Box to specify phenotype (variable) used in last GSEA-R to get Summary Results. This function ask the user to specify the phenotype (variable).dialogSummary_GSEA
Display matrix in tcltk tabledisplayInTable
Get cases for selected Studies. The Cases are the descrption of the samples from patients. The samples can be subdivided by the type of assays as, sequencing, CNA, Mutation, Methylation.getCases
get Cases and Genetic Profiles of selected Studies.getCasesGenProfs
get Circos Layout for selected studies and selected dimensionsgetCircos
get matrix with clinical from filegetClinicalDataMatrix
get Clinical Data for Multiple Cases. User needs to select at least one case to run this function. Get clinical data for more one or multiple cases.getClinicData_MultipleCases
Get gene correlation for multiple dimensions.getCor_ExpCNAMet
Built Expression Set (eSet) from profile data.geteSet
get mutation frequencygetFreqMutData
get Profile (GCT file) and Phenotype (CLS file) Data from Disease.getGCT_CLSfiles
get GCT and CLS example files.getGCTCLSExample
get matrix with gene expression from filegetGeneExpMatrix
User needs to specify which gene is interesting to get genomic cancer data. The gene must be with Symbol and one gene by line.getGeneList
get Gene List from examples. User can select one from available gene listgetGeneListExample
get gene list from MSigDBgetGeneListFromMSigDB
get Genes ClassifiergetGenesClassifier
Get successively trees of genes list for multiple casesgetGenesTree_MultipleCases
classify genes in tree for two phenotypes in the same case(disease).getGenesTree_SingleCase
Get Genetic Profile from selected StudiesgetGenProfs
get GSEA linear modeling by studies (diseases)getGSEAlm_Diseases
get GSEA linear modeling by variables (phenotype)getGSEAlm_Variables
get dataframe in TK/TCL tablegetInTable
Get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...)getListProfData
Get profile data for more than 500 genes list.getMegaProfData
get Methylation data for multiple genesgetMetDataMultipleGenes
Reduce MSigDB size for only gene listgetMSigDB
get example of .gmt file from MSigDB (Broad Institute)getMSigDBExample
Dialog Box to Select MSigDB Files from drivegetMSigDBfile
get Mutation data for multiple genesgetMutData
Associate phenotype to Studies (cancers)getPhenoTest
Search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)getProfData
get Profles Data of multiple genesgetProfilesDataMultipleGenes
get Profiles Data for a Single Gene.getProfilesDataSingleGene
get specific Mutation data for multiple genesgetSpecificMut
get Summary results from GSEA-R (Broad Institute)getSummaryGSEA
Survival plotgetSurvival
get text in tcltk windowsgetTextWin
GSEA-R (Broad Institute)GSEA
GSEA.Analyze.SetsGSEA.Analyze.Sets
GSEA.ConsPlotGSEA.ConsPlot
GSEA.EnrichmentScoreGSEA.EnrichmentScore
GSEA.EnrichmentScore2GSEA.EnrichmentScore2
GSEA.Gct2FrameGSEA.Gct2Frame
GSEA.Gct2Frame2GSEA.Gct2Frame2
GSEA.GeneRankingGSEA.GeneRanking
GSEA.HeatMapPlotGSEA.HeatMapPlot
GSEA.HeatMapPlot2GSEA.HeatMapPlot2
GSEA.NormalizeColsGSEA.NormalizeCols
GSEA.NormalizeRowsGSEA.NormalizeRows
GSEA.ReadClsFileGSEA.ReadClsFile
GSEA.Res2FrameGSEA.Res2Frame
GSEA.ThresholdGSEA.Threshold
GSEA.VarFilterGSEA.VarFilter
GSEA.write.gctGSEA.write.gct
Search MSigDb that overlap gene listMatch_GeneList_MSigDB
Dialog box to specify Gene Symbol.modalDialog
myGlobalEnvmyGlobalEnv
OLD.GSEA.EnrichmentScoreOLD.GSEA.EnrichmentScore
Plotting two genetic profiles for one Geneplot_1Gene_2GenProfs
plot correlation of two genes expressions.plot_2Genes_1GenProf
model plotting with tcltkplotModel
bind non equal rowrbind.na
The main function to run GSEA-R from Broad InstituteRun.GSEA
Setting work Directory and output folders.At starting window, user needs to set work directory for output data. The function is foud in File menu.setWorkspace
S3 method to test cBioPortal connectiontest.CGDS
Testing checked appropriate Cases for appropriate Genetic profiles.testCheckedCaseGenProf
Unify row names in data frame with the same order of gene list.UnifyRowNames